- ChimeraX-users - RBVI Mailing Lists

Animation feature in ChimeraX?
by Eric Pettersen 21 Nov '20

21 Nov '20

> Begin forwarded message: > > From: "Tweten, Rodney K. (HSC)" <Rodney-Tweten(a)ouhsc.edu> > Subject: Animatin feature in ChimeraX? > Date: November 20, 2020 at 10:05:00 AM PST > To: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> > > > Hi, > I have used Chimera for years for my publications and for generating animations for lectures and invited talks. I found the animation feature incredibly easy to use and intuitive. However I did not find a similar feature in ChimerX. I read about the Morph command but to me this seems much more complicated to use and much less intuitive. Is there a graphical interface to the Morph command or is this going to remain a command line feature only? I often use the animation feature of chimera to morph between two structural states, which is really easy. > Cheers, > Rodney Tweten, Ph.D. > George Lynn Cross Professor > Presidential Professor > > "Anti-intellectualism has been a constant thread winding its way through our political and cultural life, nurtured by the false notion that democracy means that my ignorance is just as good as your knowledge.” > Isaac Asimov > > BMSB-1053 > 940 Stanton L. Young Blvd. > The University of Oklahoma Health Sciences Center > Oklahoma City OK 73104 > USA > Work phone: 405 271-1205 > Web page: https://basicsciences.ouhsc.edu/mi/Faculty-and-Staff/Primary-Faculty/rodney… <https://basicsciences.ouhsc.edu/mi/Faculty-and-Staff/Primary-Faculty/rodney…> > Skype: toxlab1

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ChimeraXClassifier platform attribute
by Daniel Esteban Palma Igor 21 Nov '20

21 Nov '20

Hi, I have a command that will work in mac and linux but not in windows, Should I create a separate ChimeraXClassifier for linux and mac with the corresponding platform attribute or there is a way to create only one ChimeraXClassifier for both? Regards, Daniel Palma Igor

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Transparency for atoms selected only
by Gabriele Cerutti 21 Nov '20

21 Nov '20

Hello, I am trying to display transparency only for selected residues in my protein model but I am having a hard time trying to restrict the transparency only to the selected set of atoms (it sets the transparency to all residues). Do you have any suggestions and/or examples about this? Thanks, Gabriele

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Saving biomt record for generated icosahedral
by Moustafa, Ibrahim M. 20 Nov '20

20 Nov '20

Hi all, I built a full icosahedral model from ASU in chimeraX, how can I save the coordinates and BIOMT record of the generated full-model? Thanks for helping. Ibrahim

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Re: [chimerax-users] [Chimera-users] color by zone in chimeraX
by Elaine Meng 20 Nov '20

20 Nov '20

Hi Pranav, I’m Cc'ing the chimerax-users(a)cgl.ucsf.edu list (recommended for ChimeraX questions). I believe the problem is that when coloring the chains you are using “target c” which means to color only cartoons, whereas coloring by zone uses the atom colors. Since you only colored the cartoons, the atoms probably still had heteroatom color-coding. If you use “target ac” instead (even if the atoms aren’t shown), then as long as the color zone distance is big enough, I think you will get the color zones you expect. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 20, 2019, at 10:54 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: > > Hi Elaine and Co., > > I am trying to color a virus map with the relevant pdb file, the > series of commands I am running are as follows, > open virus.mrc > open virus.pdb > color /A plum target c > color /B lightgreen target c > color /C dodger blue target c > color zone #1 near #2 dist 3 > However, the resultant surface is rendered in splotches of red and > blue, which leads me to think the it is coloring the surface using > atom type. Could you tell me how I can get Chimera X to color the > surface using the colors of the chains only? FYI, color by zone works > flawlessly in chimera. > > Cheers, > Pranav

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tips on how to use the "bond rotation" right mouse tool
by M. Elizabeth Stroupe 19 Nov '20

19 Nov '20

Hi all, I am working on a little side project to use ChimeraX with high school students to explore protein structures. I am looking for tips on how to make the program as intuitive as possible! I can't seem to make the "bond rotation" tool work easily. I gather you should be able to just highlight that, depress the right button, and move the mouse over the bond you want to move. Sometimes it works and sometimes it doesn't. What am I doing wrong? (and other tips besides having students do some of your tutorials before starting the activity would be very welcome!) Thank you! Beth

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General question about MODELLER
by Moradkhan, Tiglath A 19 Nov '20

19 Nov '20

Hi I have a question about using MODELLER. I've built models of a protein that I'm currently studying and wanted to know if it's necessary to minimize regions of the protein that may have poor quality based on the QMEAN score. Or does MODELLER minimize these regions when building homology models? Thanks Tiglath

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question about lighting options
by Ryan Cammarota 18 Nov '20

18 Nov '20

Hi, I am wondering whether there is a simple way in ChimeraX to set one point (or atom) as a light source, which could allow for the shadows cast by the surrounding atoms to be visualized? Thanks for your help, Ryan

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sequential coloring of a range of residues
by Daniel Larsson 17 Nov '20

17 Nov '20

Hi, I have trouble coloring only a narrow range of residues (1-10) in one chain (P) of one model (#18). I've tried a few options: color sequential #18/P:1-10 This colors the entire chain P in rainbow colors (equivalent to atom selection #18/P). color sequential #18:1-10/P This colors _all_ residues of all chains in model #18 -- except of one chain which lacks residues 1-10. I also tried with the "rainbow" synonym. When this failed, I tried coloring according to the residue number: color byattribute r:number #18/P:1-10 This throws an error "Unknown/unregistered Residue attribute number", although number should be an attribute of residues according to this page: https://www.cgl.ucsf.edu/chimerax/docs/user/attributes.html#residue Am I doing something wrong? Is this feature not implemented yet? Is there a work-around? Regards, Daniel N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Command development
by Eric Pettersen 17 Nov '20

17 Nov '20

For any developers that will be implementing their own commands, we have put up a page about the considerations to think about when deciding on the command name and syntax, here: Command Style Guide — ChimeraX 1.2 documentation <https://www.cgl.ucsf.edu/chimerax/docs/devel/command_style.html> --Eric Eric Pettersen UCSF Computer Graphics Lab

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Atom specifier of manually selected group
by André Graça 17 Nov '20

17 Nov '20

Hi, I was wondering if there is any command that allows to list the atom specifiers for manually selected atoms using the ctrl drag and drop method. If there is one, I did not manage to frame my question properly to find it in the documentation, and I would appreciate some guidance. Thank you, André Graça

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Default movie image directory
by Daniel Asarnow 15 Nov '20

15 Nov '20

Hi, What is the default image directory when rendering on a movie on OS X? ChimeraX crashed while I was rendering (due to running out of space) and it seems like the images are taking up a lot of space somewhere. Thanks, -da

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[new-map-options] Error when using the "subregion" option
by Arthur Ecoffet 13 Nov '20

13 Nov '20

Dear ChimeraX developers, When using the "subregion" option for different map-related functions (volume morph, volume copy) I encountered the following error : *ValueError: could not broadcast input array from shape (150,150,150) into shape (151,151,151)File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\map\volume.py", line 982, in writable_copy*g.array*[:,:,:] = self.region_matrix(r) *If you want to reproduce the error, I worked on EMDB22000 and I typed in the console : *volume copy #1 subregion 150,150,150,300,300,300 *alternatively *volume morph #1 #2 subregion 150,150,150,300,300,300 * raises the same error. I tried on two versions of ChimeraX (including the last stable from September) and got the same error twice. Would you have any idea how to solve this? Thanks very much, Best, Arthur

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ChimeraX
by Reed, Scott 13 Nov '20

13 Nov '20

Helo, I am interested in getting a copy of the ChimeraX GitHub repository. I have some python code running on chimera that I would like to update to ChimeraX. Thanks, Scott Scott Reed scott.reed(a)ucdenver.edu<mailto:scott.reed@ucdenver.edu> https://ucdenver.zoom.us/j/3152346473

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Selecting a webcam
by Lewandowski, Jozef 13 Nov '20

13 Nov '20

Hi, If I have multiple webcams installed on my laptop how would I select a specific webcam to use with the webcam command? Thanks, Józef

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Clipping Map | Slices in Plane Flattening to white
by Anderson, Jacob 13 Nov '20

13 Nov '20

Dear ChimeraX Developers and Users, When I slice a colored map (not model), the portion of the map cut by the plane are flattened to white. Is there a way to make the section cut by the plane the same color as the map at that location? I include an example here. Ideally, we would like for these white areas to be the orange color of the map here. And in the bottom right, pink. [cid:21ec6d86-961b-4d86-81c4-c183a5da3447] ~jacob

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change color for map slices
by Gui, Miao 13 Nov '20

13 Nov '20

Dear chimeraX team, I have some issues when coloring a cryo-EM map. I firstly colored a map gray, then fitted the models in the map and colored the map by zone. I'd like to generate a cross-section slice, but the slice color is always white. Please see the attached image for example, the green surface color is good, but the slice is white. Is there a feature I could use to cap the slices with colors? Thanks. Best wishes, Miao

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Re: [chimerax-users] Help please on how to create a homodimer with different chain IDs using sym command
by Elaine Meng 10 Nov '20

10 Nov '20

Dear Scott, That's great! We like to hear that ChimeraX is used in teaching. To get the dimer, I guess you used open 2zhg sym #1 assembly 1 (since "sym #1" merely reports the assemblies available and does not add the other half). Then, the first half is model #1 containing chains A,B and the second half is model #2 also containing chains A,B. You can see you have two models in the "Models" panel on the right. Thus you can refer to the two A chains separately in the command line as #1/A and #2/A, or the entire models as #1 and #2. Command-line specification: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> An alternative is to fetch the biounit directly, e.g. open 2zhg from pdbe_bio maxassemblies 1 In that case the DNA chains are A and AA and the protein ones are B and BA. You can see this information in the Log when the file is opened. For explanation of fetching and its options: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> Unless including private data, it's better to send questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) rather than to me personally... then others may benefit, and the messages are kept in a searchable archive. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 10, 2020, at 9:43 AM, Scott White <S.A.WHITE(a)bham.ac.uk> wrote: > > Dear Elaine, > > I am using ChimeraX for teaching. I want to be able to instruct how to create a homodimer, but to manipulate the separate chains, eg colour them differently. > > example: > open 2zhg (asu, one half of a homodimer) > sym #1 (create the other half) > > but both polypeptide chains are labelled Chain A. If I select "sel \a" I get the whole model. If I use right-mouse-button select by clicking, I get the atom in both chains selected. > > How can I manipulate the two polypeptide chains independently? I've tried playing with the various sym options, but I can't get that to work. I have tried using "split" command, but that splits the polypeptide and DNA chains into separate submodels, as expected. It won't split the two chains A into a A and C, for example. > > Any guidance please? > > I know I could save the file and use a file editor such as vi, but this is a class for students and I was hoping to do it all by ChimeraX. > > I'm working with ChimeraX version 1.0 > > thanks for your help, > Scott

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Re: [chimerax-users] Assistance: ChimeraX save scene
by Guillaume Gaullier 10 Nov '20

10 Nov '20

Priyanka, Sorry, but I don’t know the answer to your question off the top of my head, and I won’t have time to figure it out this week. As I already recommended, please email the list chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (copied to this email) and not me (or anybody else) individually: you will get answers faster this way, because the people who develop ChimeraX monitor this mailing-list and are really good at answering questions; it is also more useful for everybody, since questions and answers sent to the list get archived and become searchable on the list’s website. I hope somebody can help you solve your problem soon. Good luck. Guillaume > On 10 Nov 2020, at 04:36, Priyanka Abeyrathne <pabeyrat(a)gmail.com> wrote: > > Hi Guillaume, > > I used the "view name myview" and "view myview" to save the scene in ChimeraX. It worked only one time as scene saved as ---.cxs file. I tried the scene command again but it didn't work. Any suggestions? > > Thanks a lot. > Priyanka > > On Mon, Oct 12, 2020 at 3:41 AM Guillaume Gaullier <guillaume(a)gaullier.org <mailto:guillaume@gaullier.org>> wrote: > Hi Priyanka, > > If what you need is a command that can restore the camera’s position to a previously saved state after you moved it, then this should be helpful: > > 1. set the scene the way you want it > 2. run command "view name myview" ("myview" can be any name); what this does is assign a name to the current view (camera settings) > 3. rotate or translate, move around, etc. > 4. run command "view myview", which should reset the camera settings to what they were when you did step 2 above > > I believe named views are saved with the session, so you should be able to use them even after you save and close, then reopen your .cxs file. > > You will find more details in the documentation, with command "help view". Also here: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > I hope this helps, > > Guillaume > > >> On 11 Oct 2020, at 22:10, Priyanka Abeyrathne <pabeyrat(a)gmail.com <mailto:pabeyrat@gmail.com>> wrote: >> >> Hi All, >> >> Is there a save scene command in ChimeraX? >> >> Thanks, >> Priyanka >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >

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Assistance: scene
by Priyanka Abeyrathne 10 Nov '20

10 Nov '20

Dear All, Is there a save scene command in ChimeraX? Thanks, Priyanka

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right mouse modes on home tab
by Anthony James Schaefer 06 Nov '20

06 Nov '20

Hello, Would it be possible to allow certain right mouse mode buttons to be added to the "Home" tab on the toolbar, like you can do with other buttons? Thanks, Tony

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Question about ChimeraX
by Diego Fernando Leon Vargas 06 Nov '20

06 Nov '20

Greetings, Hope that you're doing well. Currently, I'm using dock6 to develop some experiments as you understand this software needs Chimera as visualizator, however, I was tried to create a surface for a specific protein and this software generated an issue because my protein exceed the size, so I read the possible solutions and one of them is using ChimeraX, nevertheless, I downloaded ChimeraX and I was able to create the surface, however, I didn't find an option to save this surface and I didn't find and option to create a DMS file. Then I have already read your user guide to ChimeraX but I didn't find information about how to create the DMS file, or how to save the surface information in any format that Chimera would be able to open, because I found a lot of differences between "Structure editing" option in Chimera and ChimeraX, then I'm requesting your help to create the DMS file using ChimeraX or indicanting me a way to save the surface information to use it later using Chimera. Thank you so much for your help. Kind regards, B.Sc Diego Fernando León Vargas, Ph.D (c) -- Cordialmente, *Q.F Diego Fernando León Vargas* Estudiante - Doctorado en ciencias farmacéuticas Grupo de estudios en síntesis y aplicaciones de compuestos heterocíclicos - (GESACH) Facultad de Ciencias Universidad Nacional de Colombia Sede Bogotá -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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Add documentation to Bundle Sample Code
by Daniel Esteban Palma Igor 05 Nov '20

05 Nov '20

Hi, I have encountered very useful the Bundle Sample Code ( https://www.cgl.ucsf.edu/chimerax/docs/devel/writing_bundles.html) as a reminder of how to do a bundle, the only thing that I would like being added to it is an example documentation. Regards, Daniel Palma Igor

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Assistance
by Priyanka Abeyrathne 03 Nov '20

03 Nov '20

Hi ChimeraX developers, Could someone let me know after the superposition of the cryo-EM map in PDB, what is the command to see PDB through the cryo-EM map densities (how to make cryo-EM map transparent without changing domain color in the cryo-EM map to see the PDB)? Thank you. Kind regards, Priyanka

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New icosahedral lattices relevant for viruses
by Tom Goddard 30 Oct '20

30 Oct '20

Hi Colin, Toni, I added your new icosahedral virus lattices to the ChimeraX hkcage command using your GitHub code. I changed your "alpha" parameter that chooses the lattice type from a number (you used 1-8) to instead a string that can be one of standard, standard-dual, rhomb, rhomb-dual, trihex, trihex-dual, snub, snub-dual. When the hkcage command is used with any of your lattices it logs a message so the user knows to cite your publication. Thanks for contributing this new feature! Tom > On Oct 30, 2020, at 12:04 PM, Colin Brown <colintravisbrown(a)gmail.com> wrote: > > Hi Tom, > > The repository is now public. Let me know if you’d like to be added as a collaborator as we continue revising the bundle. > > Thank you, > Colin Brown > From: Tom Goddard <goddard(a)sonic.net> > Sent: Friday, October 30, 2020 10:46:39 AM > To: Antoni Luque Santolaria <aluque(a)sdsu.edu> > Cc: chimera-dev(a)cgl.ucsf.edu <chimera-dev(a)cgl.ucsf.edu>; Colin Brown <colintravisbrown(a)gmail.com> > Subject: Re: [chimera-dev] question: development of a new icosahedral tool to include new lattices relevant for viruses > > Hi Toni, > > Thanks! I would like to put your improved hkcage command into ChimeraX. The github link to the hktest bundle gives a 404 error "not found" in the web browser. Maybe your repository is private? If your source code is clean and maintainable I can just put it in ChimeraX, no need for a meeting. I do not think I should be a co-author as I have contributed very little. > > Tom > > >> On Oct 30, 2020, at 6:38 AM, Antoni Luque Santolaria <aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>> wrote: >> >> Dear Tom, >> >> Here are some updates and questions regarding the new hkcage bundle: >> >> 1. The new bundle now generates the 8 icosahedral lattices (hexagonal, trihexagonal, snub hexagonal, and rhombitrihexagonal), including regular and dual as published in Tawrock and Luque, 2019. Our next step is to publish the method, for example, in PeerJ Computer Science. We based our approach on your hkcage tool. Since the method underlying that tool was not published on a peer-reviewed journal, we would like you to be a co-author in the manuscript. Would you be interested in being a co-author? >> >> 2. As we polish the algorithm and the bundle's options for publication, we would like to incorporate changes that you consider adequate so the new hkcage tool can be integrated as a native tool in Chimera X in the near future. If this sounds good to you, we could set up a meeting to show you how the tool works and receive feedback from you about options that you consider essential for Chimera X. What do you think? >> >> 3. The current version of the bundle is available on GitHub: https://github.com/colintravisbrown/hktest <https://github.com/colintravisbrown/hktest>. The lattices are controlled by the new parameter alpha, which takes values from 1 to 8. We have used the tool to generate figures for research talks and a research manuscript, which is currently under review. In this google drive folder, you can see some of the images and movies (files named chimera_*): >> >> 4. Our project is funded by the National Science Foundation. Integrating our new tool in Chimera X is one of our Broader Impact goals. Accomplishing this task will help us secure additional funding to develop more computational methods for Chimera X and the scientific community. Your support on this end is greatly appreciated. >> >> Let me know if you have any questions. >> >> Thanks for your time, >> Toni >> >> On Fri, Jun 26, 2020 at 1:30 PM Antoni Luque Santolaria <aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>> wrote: >> Great, thanks for the info! >> >> On Fri, Jun 26, 2020 at 9:38 AM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Toni, >> >> Ok, plan sounds good. >> >> Regarding the coloring, it is usually easy to do when you have an atomic model of the asymmetric unit, you just color each chain as needed. That requires no additional capabilities in Chimera / ChimeraX. To generate the icosahedral layout from the asymmetric unit (1/60 of capsid) use the sym command. To color a cryoEM map the easiest approach is to use the "color zone" capability to color the map according to the atomic model. It is only when you don't have an atomic model for the map that the coloring gets tricky. That is a rare case since usually the first thing that is done with these maps is to fit an atomic model. That herpes simplex virus image I sent was one of those rare cases, the researchers were studying the virus portal and did not include atomic models in their publication. So developing easier coloring may not be needed. >> >> Tom >> >> >>> On Jun 25, 2020, at 6:06 PM, Antoni Luque Santolaria <aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>> wrote: >>> >>> Thanks, Tom. >>> >>> 1) The user interface will not be essential for the research that we'll be carrying out in the short term, but it's something that I think it would be beneficial in the longer run. Whenever you have a chance to port the interface from Chimera to Chimera X let us know, and we'll adapt it for the extended hkcage. In the meantime, we'll focus on extending the hkcage tool to work through the command line. >>> >>> 2) Coloring the proteins in relation to hkcage as in the example that you shared would be ideal. In fact, for herpes, the trihexagonal lattice would show trimers that are missing in the color scheme of the image that you shared. Our initial goal is to focus on viruses deposited in viperdb because they have associated pdb files, but we would also like to include some cryo-em capsids in the analysis because there are many more capsid architectures that must to be reanalyzed. We'll follow the protocol that is described in the link that you shared with us. >>> >>> Best, >>> Toni >>> >>> On Thu, Jun 25, 2020 at 9:32 AM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>> Hi Toni, >>> >>> That all sounds good. Yes the link you found is our svn source code for cages.py. Sorry, I accidentally gave you the https link which takes a password and allows checking in changes to the code. >>> >>> The additional options to the hkcage command should be no trouble. It will be pretty obvious how to add them in ChimeraX. In Chimera the code may be harder to fathom, but Colin can ask when stuck on anything. >>> >>> The user interface panel is the most work of what you describe. The current Icosahedron Surface tool in Chimera does not offer the hkcage options, just a plain icosahedron. The hkcage command was developed after that user interface and never got incorporated in. For that user interface window Chimera and ChimeraX will be completely different because Chimera uses the Tk window toolkit while ChimeraX uses the Qt window toolkit. I suggest giving priority to the ChimeraX version of that tool, although the plain icosahedron user interface has not been ported to ChimeraX yet. Possibly I can port it to ChimeraX making all the Tk to Qt changes as a starting point for Colin. Probably I would not have time to do that until mid-July. The Chimera icosahedron surface tool has a subdivision parameter that divides the facets into smaller triangles. The current hkcage does not support that and some extra code would be needed to compute such subdivisions of the hexagons, pentagons, .... >>> >>> It may also be interesting to think about how to color electron microscopy maps to show the virus capsomere arrangement, for example as in this image >>> >>> https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/herpes/herpes.html <https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/herpes/herpes.html> >>> <emd1307.jpg> >>> ChimeraX hkcage docs >>> >>> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/hkcage.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/hkcage.html> >>> >>> Chimera hkcage docs >>> >>> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html> >>> >>> Chimera icosahedron surface docs >>> >>> https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/icosahedron/icosa… <https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/icosahedron/icosa…> >>> >>> Tom >>> >>> >>>> On Jun 25, 2020, at 9:02 AM, Antoni Luque Santolaria <aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>> wrote: >>>> >>>> Hi Tom, >>>> >>>> 1. Thank you for the quick response and clear instructions. I wasn't aware of ChimeraX. I just installed it, and it looks fantastic. >>>> >>>> 2. Colin Brown (in CC) is a master student in the lab who will be leading the efforts to develop the new icosahedral tool over the summer. He will contact you if we have any questions during the development process. >>>> >>>> 3. I wasn't able to access the second link that you shared with us. It requires a username and password. But I found the cages.py in this other link: http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/contrib/IcosahedralCag… <http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/contrib/IcosahedralCag…> Is it the same code? >>>> >>>> 4. The extension that we have in mind would include an option, as you suggest, to identify the lattice (h, t, s, r,...), an option to indicate if the construction uses the regular (hexagons, pentagons) or dual (single tile) blocks, and a third parameter for lattices that have a degree of freedom (see for example Figure 5a in Twarock and Luque, 2019). We would also like to add a panel to control the options manually like in the icosahedron tool. The goal of this gui panel would be to facilitate users to modify the radius, sphere factor, and other options on the fly to obtain a good visual agreement with the viral structure or macromolecular complex of study. Let us know if this would be reasonable. >>>> >>>> Best, >>>> Toni >>>> >>>> On Wed, Jun 24, 2020 at 2:30 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>> Hi Toni, >>>> >>>> Neat! I wrote the hkcage code and I think adding your 3 additional series t,s,r to that command would be the way for researchers to get the most use out of it. It could simply be adding one more option to that command that specifies the series. The code that would be needed is Python that computes the vertex coordinates, a triangulation (a list of 3-tuples of vertex indices), and an edge mask that says which of the triangle edges should be hidden (one integer per triangle with 3-bits 0x1, 0x2, 0x4 indicating if the triangle edge should be shown). I could incorporate your code into the Chimera and ChimeraX distributions and we would credit you cite your paper in the documentation. I think it would be quite easy for you to simply modify the cage.py code in your Chimera or ChimeraX distribution, do all the testing, write a bit of documentation describing the new option -- send that to me and I will get it into the daily builds and subsequent releases. >>>> >>>> ChimeraX is the successor of Chimera and ChimeraX 1.0 was just released. Most researchers are still using Chimera instead of ChimeraX but we expect that to transition over the next few years, so I would suggest making your addition to the ChimeraX code. But you can make the additions to ChimeraX or Chimera and I can move it to the other if you like, the hkcage code for the two is nearly identical. ChimeraX uses Python 3 while Chimera uses Python 2. >>>> >>>> https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/bundles/hkcage/src/cage… <https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/bundles/hkcage/src/cage…> >>>> >>>> https://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/IcosahedralCage/… <https://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/IcosahedralCage/…> >>>> >>>> Tom >>>> >>>> >>>>> On Jun 24, 2020, at 8:49 AM, Antoni Luque Santolaria <aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>> wrote: >>>>> >>>>> Dear Chimera development team, >>>>> >>>>> My lab is interested in developing (or extending) a new version of the hkcage command in cages.py to include the different icosahedral lattices that have been recently discovered and have important implications for viral structures (see Twarock and Luque, Nature Communications, 2019). We would like to receive advice on what would be the best approach to help integrate the tool to be used and shared with the Chimera community. Would it be better to extend hkcage? Generate a new function? Integrate the function in cages.py? Generate a different python script? >>>>> >>>>> My lab (https://www.luquelab.com/ <https://www.luquelab.com/>) is part of the Viral Information Institute at San Diego State University (https://viralization.org/ <https://viralization.org/>) and recently discovered, in collaboration with Prof. Reidun Twarock (The University of York), a new set of icosahedral lattices that describe previously uncharacterized viral capsid structures (https://www.nature.com/articles/s41467-019-12367-3 <https://www.nature.com/articles/s41467-019-12367-3>). My lab's goal is to develop a tool in Chimera that reflects these new geometries and helps us analyze viral capsids and other complexes with icosahedral symmetry. We would also like to facilitate the scientific community to use this tool in Chimera. This project will be developed as part of an NSF award. >>>>> >>>>> Please let us know the best way to proceed. >>>>> >>>>> Thanks, >>>>> Toni >>>>> >>>>> >>>>> -- >>>>> Antoni Luque, PhD >>>>> http://luquelab.com <http://luquelab.com/> >>>>> Assistant Professor >>>>> Department of Mathematics and Statistics >>>>> Viral Information Institute >>>>> San Diego State University >>>>> >>>>> Office: GMCS 514 >>>>> Phone: 619 594 7244 >>>>> email: aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>_______________________________________________ >>>>> Chimera-dev mailing list >>>>> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >>>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev> >>>> >>>> >>>> >>>> -- >>>> Antoni Luque, PhD >>>> http://luquelab.com <http://luquelab.com/> >>>> Assistant Professor >>>> Department of Mathematics and Statistics >>>> Viral Information Institute >>>> San Diego State University >>>> >>>> Office: GMCS 514 >>>> Phone: 619 594 7244 >>>> email: aluque(a)sdsu.edu <mailto:aluque@sdsu.edu> >>> >>> >>> -- >>> Antoni Luque, PhD >>> http://luquelab.com <http://luquelab.com/> >>> Assistant Professor >>> Department of Mathematics and Statistics >>> Viral Information Institute >>> San Diego State University >>> >>> Office: GMCS 514 >>> Phone: 619 594 7244 >>> email: aluque(a)sdsu.edu <mailto:aluque@sdsu.edu> >> >> >> -- >> Antoni Luque, PhD >> http://luquelab.com <http://luquelab.com/> >> Assistant Professor >> Department of Mathematics and Statistics >> Viral Information Institute >> San Diego State University >> >> Office: GMCS 514 >> Phone: 619 594 7244 >> email: aluque(a)sdsu.edu <mailto:aluque@sdsu.edu> >> >> -- >> Antoni Luque, PhD >> http://luquelab.com <http://luquelab.com/> >> Assistant Professor >> Department of Mathematics and Statistics >> Viral Information Institute >> San Diego State University >> >> Office: GMCS 514 >> Phone: 619 594 7244 >> email: aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>

1 0

Request for technical clarification on your software to enhance for 3D Visualization
by rameshsj＠ideasahead.in 30 Oct '20

30 Oct '20

Hi, Greetings from Ideas Ahead AV Solutions Pvt. Ltd. We are working on a project to provide a solution for 3D Visualization on a CAVE environment to one of our customer in India who are working on molecular structure and Genomics. We have few queries w.r.t to the functionality of your software. Hence kindly request you to please clarify on the same for us to proceed further. 1. Does your software files supports 3D stereoscopic visualization and the CAVE environment (multiple projection system)? 2. Please let us know what are the minimum hardware specification that is required along with the graphics card to run your software models? 3. Does your software support ART Tracking environment? 4. For visualization does the software needs TechViz 3D Real Time Visualization software or can it run independently on the cable? ____________________________________________________________________________ __________________________________________ Ideas Ahead AV Solutions Pvt. Ltd. the India's leading Audio Visual systems integrator and the right technical Solution provider along with technical support & service. The Ideas Ahead team has an unrivalled knowledge of providing turn-key solutions for VR/AR/MR, Visual Simulation, 3D theatre & Auditorium, audio visual technology. Ideas Ahead specifies designs, installs, integrates, maintains and operates complex audio visual systems for Corporates, OEMs, Defence labs, Educational institutions, Department of Space and Public sector Organizations in India. We have been an established and popular company with an excellent track record for the best customer satisfaction. We have never compromised on the quality and the services provided to the customer. Please find the business areas of Ideas Ahead is mentioned below. Business Verticals: * Virtual Reality & 3D Visualization with CAVE * Audio-Visual & Controls * Visual Simulation in Aerospace, Military & Marine Engineering * 3D theatre & Auditorium * Customer Experience Centers * Services & AMCs ____________________________________________________________________________ _______________________________________________ Your assistance would definitely help us to understand the software better for further projects and contribute back to the ecosystem. Looking forward to your kind clarifications on the requested queries. Thanks, With Best Regards, S J Ramesh Kumar I General Manager - Key Accounts Ideas Ahead AV Solutions Pvt. Ltd. #436, 9th Main, HRBR Layout Kalyan Nagar 1st Stage, Bangalore - 560 043. India (M)+91 81979 66677 / (Off) +91 80 4098 0201/202/203 Skype id: rameshsj Website: www.ideasahead.in <http://www.ideasahead.in/> "Ideas Ahead India's leading Audio Visual Systems Integrator & Service Provider excels at complex requiring converged AV & IT Solutions" <https://tc3.shftrk.com/e/3k5GdZEo0oPD6PEm/KY5nl8znAEr8bNg1/9GO6XdBNgPedZQM0 >

2 2

Deleting unmodelled termini
by mailman-bounces＠cgl.ucsf.edu 29 Oct '20

29 Oct '20

From: "Moradkhan, Tiglath A" <tmoradkhan(a)csus.edu <mailto:tmoradkhan@csus.edu>> Subject: Deleting unmodelled termini Date: October 29, 2020 at 4:48:14 PM PDT Hi I've read the delete command documentation to delete unmodelled termini and rerun Modeller, but I'm having a hard time trying to delete the C-terminal end of the models. Say that the first time Modeller wasn't able to model residues 1-67 and 209-267 because these regions don't align with the template structures. Here is the command (all the returned models are labeled as 3.1-3.4) delete #3/A-B: 1-67,209-267 Is this right? I also tried deleting these residues before running Modeller with no success. I'll be very glad for some help. Thanks Tiglath

2 1

Set atom coordinates by command?
by Jeschke Gunnar 29 Oct '20

29 Oct '20

Hi all, is there a way to set atom coordinates by a command? setattr spec atoms coord value appears to accept only one double argument and sets x, y, and z to this number. Neither space-separated nor comma-separate lists of three values appear to work. Kind regards Gunnar --- Prof. Dr. Gunnar Jeschke ETH Zurich Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 2 CH-8093 Zurich Switzerland www.epr.ethz.ch

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Worms?
by Boris Steipe 28 Oct '20

28 Oct '20

Worm plots is one of the still missing features. I probably have the following options (though I haven't actually tried any): - compute my own spline and place a dense string of spheres - compute my own spline and place alternating spheres and cones - place pseudoatoms and compute a surface with a small probe radius - wait until Chimera's worm plot arrives in ChimeraX. Or is there a better way? Thanks! Boris

2 2

Set different colors for each letter like in chimera
by Siyu Chen 28 Oct '20

28 Oct '20

Dear chimerax developers, I was trying to color my labels in chimerax using commands, but it will be too tedious for me to create different labels for each letters, color them differently then align them by fine-tuning the x/y positions. I remember in chimera I was able to call out an window and within that, I can conveniently edit my texts and colors, and save it as a label file. Does chimerax still offer the similar function? Or if there is any equivalent way to achieve that easily? Thanks a lot for your help! Best, Siyu

3 3

Using ChimeraX Modeller interface
by Moradkhan, Tiglath A 26 Oct '20

26 Oct '20

Hi My name is Tiglath and I'm trying to use ChimerX Modeller interface to build a dimer model of a protein I'm currently studying. I first tried to run a BLASP search to find templates but it seems that in ChimeraX, this works differently than in Chimera. In the user guide it says that if the query is a sequence whose structure hasn't been determined, then it's not necessary to specify particular chains. However, when I try running the BLAST search it doesn't do anything. It seems that it is necessary to specify a chain number. But how is this possible if I don't know the template for the target sequence? Am I missing something? Also, I'm a little bit unsure how the Modeller interface works for building dimers. I would be very glad for your help. Thank you Tiglath

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Markers from CMM
by Scott, Brandon L. 26 Oct '20

26 Oct '20

Hello all, When loading markers from a cmm file (example attached), is there a way to specify which submodel the marker goes to rather than it creating a new id? I've added the id_string to the cmm file when I created a new one which is the desired model. I hacked the following, which works, but there are hundreds of tracks so I would like to come up with an automated (and proper) way to do this. perframe "rename #2.$1 track_1 id #1.$2.2;" ranges 1,113 ranges 4,116 perframe "rename #2.$1 track_2 id #1.$2.3;" ranges 114,259 ranges 5,150 Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor Nanoscience & Nanoengineering South Dakota Mines 501 E. Saint Joseph St., Rapid City, SD 57701 724.510.1253 | Brandon.Scott(a)sdsmt.edu<mailto:Brandon.Scott@sdsmt.edu> [South Dakota Mines]<https://www.sdsmt.edu/> [South Dakota Mines on Facebook]<https://www.facebook.com/SouthDakotaMines/>[South Dakota Mines on Instagram]<https://www.instagram.com/southdakotamines/>[South Dakota Mines on Twitter]<https://twitter.com/sdsmt>[South Dakota Mines on Snapchat]<https://www.snapchat.com/add/sdsmt>

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Re: [chimerax-users] ISOLDE on Chimerax on centos8.0
by chimera-users-owner＠cgl.ucsf.edu 23 Oct '20

23 Oct '20

Hi I have just recently installed Chimerax 1.1 on my centOS 8.0 workstation and am trying to install the ISOLDE bundle thru Toolshed but I get the message "no download available for Cimerax 1.1 on Linux." how do I get around this problem Cheers Shabir Najmudin

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Re: [chimerax-users] ChimeraX hardware recommendations
by Tom Goddard 21 Oct '20

21 Oct '20

Hi Shaun, Apple will keep OpenGL graphics working well into the future. They switched to using their proprietary Metal graphics to run the macOS window system about 4 years ago, and deprecated OpenGL use, but that just means they aren't going to improve their OpenGL. Mac OpenGL drivers tend to crash when lots of graphics memory is used. We are considering using Vulkan instead of OpenGL maybe in a few years. Vulkan is an open standard and has been layered on top of Metal (called MoltenVK) and has native drivers on Windows and Linux. Also I have been testing Chimera and ChimeraX on the next macOS, called Big Sur, likely coming out in the next month. Both are working on Big Sur beta 10 released a week ago, although you need ChimeraX 1.1.1. We had to fix ChimeraX 1.1 on Big Sur because Apple changed how software finds the OpenGL library. Tom > On Oct 21, 2020, at 10:40 AM, Shaun Rawson <rawson(a)hkl.hms.harvard.edu> wrote: > > No worries, thanks for the response. As an aside to the initial question, are you expecting any issues with OpenGL for ChimeraX on Macs now that they are depreciating and pushing metal instead? > > Shaun > > On Wed, Oct 21, 2020 at 1:31 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Oops, sorry for misspelling your name. > > Tom > > >> On Oct 21, 2020, at 10:30 AM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Shawn, >> >> You are right that a MacBook with i5 CPU and 16 GB memory and Intel graphics will work fine for ChimeraX including making movies. For large molecules, for example ribosome structures with several hundred thousands atoms, or large cryoEM maps, for example 512 x 512 x 512 and up you could benefit from faster AMD or Nvidia laptop graphics (MacBook Pro), and 32 GB of memory. Another thing to consider is to keep data and ChimeraX on an SSD drive, not a spinning drive. Today's SSD drives are 30 times faster reading data than spinning drives. All Mac laptops only come with SSD drives I believe, but it is good to have enough SSD drive space that your data (like lots of cryoEM maps) does not have to reside on an external drive. Usually 512 GB SSD will do, but again if you work with lots of large data 1 TB SSD could be helpful. >> >> Sorry our ChimeraX web site is unexpectedly down this morning due to some server upgrade issue. Should be back online later today. >> >> Tom >> >> >>> On Oct 21, 2020, at 7:50 AM, Shaun Rawson <rawson(a)hkl.hms.harvard.edu <mailto:rawson@hkl.hms.harvard.edu>> wrote: >>> >>> Hi Tom, >>> >>> Just a quick question on any hardware recommendations for running ChimeraX (primarily macbook based). We have a user who is particularly interested in generating animations in ChimeraX so I was wondering if you have any specific min/recommended specs for various functionality. >>> >>> It seems to me like the standard macbook config (i5, 16GB RAM, intel graphics) should be fine for day to day operations but maybe they would need to swap to a more powerful linux workstation for the heavy lifting. >>> >>> Apologies if this is available online - currently https://www.cgl.ucsf.edu/chimerax/ <https://www.cgl.ucsf.edu/chimerax/> gives a 403 error for me. >>> >>> Thanks, >>> >>> Shaun >> >

1 0

Re: [chimerax-users] ChimeraX hardware recommendations
by Tom Goddard 21 Oct '20

21 Oct '20

Hi Shawn, You are right that a MacBook with i5 CPU and 16 GB memory and Intel graphics will work fine for ChimeraX including making movies. For large molecules, for example ribosome structures with several hundred thousands atoms, or large cryoEM maps, for example 512 x 512 x 512 and up you could benefit from faster AMD or Nvidia laptop graphics (MacBook Pro), and 32 GB of memory. Another thing to consider is to keep data and ChimeraX on an SSD drive, not a spinning drive. Today's SSD drives are 30 times faster reading data than spinning drives. All Mac laptops only come with SSD drives I believe, but it is good to have enough SSD drive space that your data (like lots of cryoEM maps) does not have to reside on an external drive. Usually 512 GB SSD will do, but again if you work with lots of large data 1 TB SSD could be helpful. Sorry our ChimeraX web site is unexpectedly down this morning due to some server upgrade issue. Should be back online later today. Tom > On Oct 21, 2020, at 7:50 AM, Shaun Rawson <rawson(a)hkl.hms.harvard.edu> wrote: > > Hi Tom, > > Just a quick question on any hardware recommendations for running ChimeraX (primarily macbook based). We have a user who is particularly interested in generating animations in ChimeraX so I was wondering if you have any specific min/recommended specs for various functionality. > > It seems to me like the standard macbook config (i5, 16GB RAM, intel graphics) should be fine for day to day operations but maybe they would need to swap to a more powerful linux workstation for the heavy lifting. > > Apologies if this is available online - currently https://www.cgl.ucsf.edu/chimerax/ <https://www.cgl.ucsf.edu/chimerax/> gives a 403 error for me. > > Thanks, > > Shaun

1 0

(no subject)
by Kazan Ramy (M.) 20 Oct '20

20 Oct '20

Greetings to all, When opening a new molecule, ChimeraX automatically apply a color to my molecule. I know how to modify the colors, which is very fun especailly using the command line but also very time consuming for multi-chain molecules. I would like to impose a coloring scheme for a model by default, that way everytime I open the model the coloring is the same for the my molecule. I guess one way is to use the function key but this would be limited to a mixumum of twelve molecules and is atom-spec dependent so not very practical. Is there a way to permently save the information, maybe in the pdb file header/footer, or somewhere else? Ramy Kazan PhD Student

2 1

cartoon style atom-spec
by Daniel Asarnow 20 Oct '20

20 Oct '20

Hi, When I use cartoon style with an atom spec, ChimeraX reports "expected a keyword" error. This is the "licorice" example from the documentation, which only works without an atom spec. car style protein modeh default arrows f xsect oval width 1 thick 1 car style #6/H protein modeh default arrows f xsect oval width 1 thick 1 Is my syntax wrong? Thanks, -da

2 2

Access to git repository
by Tomris, I. (Ilhan) 19 Oct '20

19 Oct '20

Dear sir/madam, At the moment I am utitilizing ChimeraX to render 3D images of lightsheet data I have obtained (see attachment of 3D render). It is a pretty nice software package, although there is something I would like to implement into chimerax. A bounding box/outline box with gridpoints on it to indicate the size of the rendered volume, additionally I would also like to implement a scalebar of some sort. Hence I was wondering whether I could get access to the git repository so I could attempt to use the "Outline box" already present and put grid points on it? [cid:ab15abd2-e188-42fa-ae88-eedbeae317dd] Kind regards, Ilhan

2 1

Re: [chimerax-users] Assistance: ChimeraX save scene
by Guillaume Gaullier 19 Oct '20

19 Oct '20

Hi Priyanka, Sorry for this late reply. I am copying the chimerax-users list (if you had sent your last email to the list, somebody else would maybe have answered you earlier; also a good idea to communicate through the list because all emails are archived and that sometimes enables people to find answers to their questions directly by searching the archives). Regarding you question about colors: in ChimeraX, the command "color list" will print in the log a list of colors with their names. Color names made of more than one word are listed twice: spelled with and without a space. I just checked that if you spell color names as they are listed by this command, it works. So, in your case, try spelling it "royalblue" with no space. Regarding your second question, I think this should work, but I am not quite sure what you are trying to do: volume zone #1 nearAtoms sel range 2 newMap true minimalBounds false in which #1 is your main map (so not necessarily #1 in your session, use the correct model number for your map as seen in the model panel) and sel is a selection of the atoms of interest (in your case "/A" for chain A), "range 2" is how many angstroms away from the model atoms you want to perform the map cut-out (I put 2 arbitrarily; try different values and use what you think is best for what you are trying to do), "newMap true" tells it to generate a new object for this map cut-out (it should show up in the model panel after you run the command) and "minimalBounds false" tells it to keep the same box size as your original map (if set to true instead, it will choose the minimal box size that encloses your map cut-out; not sure which one you need, but keeping the same box size should be safe). Once you have this, you can write this map cut-out to a file with the following command: save /path/to/your/new/map.mrc models #2 (replace #2 by the correct object identifier for your new map, as reported in the model panel). I hope this helps, Guillaume > On 16 Oct 2020, at 03:31, Priyanka Abeyrathne <pabeyrat(a)gmail.com> wrote: > > Hi Guillaume, > > Thank you so much for your assistance. I am going to use it soon and if I happened to have questions I will let you know. > > I have two other questions to clarify with you. > > 1. I used the following commands to color the pdb > seq chain /A > Then I highlighted the chain A > color sel blue > > I can see the chain A color is blue. Now ChimeraX has really nice color scheme. I tried to color chain A to royal blue (#4169E1 26,41,88). When I use the above commands > seq chain /A > highlighted the chain A > color sel royal blue > Didn't change the color blue to royal blue. Cod you please assist me how to fix theis? > > 2. pdb of the protein has three chains (A, B and C). I have a cryo-EM structure of the same protein. How can I extract only chain A density from cryo-EM structure. I think I have to use a segment map command. Could you please assist me how to do this in ChimeraX. > > Thank you so much. > Kind regards, > Priyanka > > > > On Mon, Oct 12, 2020 at 3:41 AM Guillaume Gaullier <guillaume(a)gaullier.org <mailto:guillaume@gaullier.org>> wrote: > Hi Priyanka, > > If what you need is a command that can restore the camera’s position to a previously saved state after you moved it, then this should be helpful: > > 1. set the scene the way you want it > 2. run command "view name myview" ("myview" can be any name); what this does is assign a name to the current view (camera settings) > 3. rotate or translate, move around, etc. > 4. run command "view myview", which should reset the camera settings to what they were when you did step 2 above > > I believe named views are saved with the session, so you should be able to use them even after you save and close, then reopen your .cxs file. > > You will find more details in the documentation, with command "help view". Also here: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > I hope this helps, > > Guillaume > > >> On 11 Oct 2020, at 22:10, Priyanka Abeyrathne <pabeyrat(a)gmail.com <mailto:pabeyrat@gmail.com>> wrote: >> >> Hi All, >> >> Is there a save scene command in ChimeraX? >> >> Thanks, >> Priyanka >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >

2 1

Set transparency on DNA stubs
by Siyu Chen 16 Oct '20

16 Oct '20

Dear chimerax developers, I am writing to ask about an issue regarding to the transparency of DNA bases. I set the double strand DNA as stubs and colored cyan, and I wanted to set it as transparent (trans 70 tar c). However, it looks like only the DNA backbones become transparent, and the bases are still bright and solid. I even tried to throw in all possible targets into the 'trans' command (acrsbpfl) and got the same looking images. I am just wondering if this is because of the style or color that makes the bases look solid? Also, do you have other suggestions to get around this issue? Thanks in advance for your time and help! Best, Siyu Chen

2 1

Chnage Chain IDs
by Kazan Ramy (M.) 13 Oct '20

13 Oct '20

Greetings to all, In UCSF Chimera tools, there's an option to change chains ID/names. Unfortunately, I can't save my model under a cif format. While in Chimera X , I can save a model under a cif format but can't change the name of my chains, or at least I'm not able to find the command for that. My main goal is to have my model under a cif format with my new naming system, any idea on how I can solve this problem? Ramy Kazan PhD Student

2 2

Assistance: ChimeraX save scene
by Priyanka Abeyrathne 12 Oct '20

12 Oct '20

Hi All, Is there a save scene command in ChimeraX? Thanks, Priyanka

3 3

Resources to get started with toolshed development
by Florian Wernert 12 Oct '20

12 Oct '20

Hi there, I'm looking forward to integrate a processing algorithm I coded into a toolshed for ChimeraX. Are there any available resources in order to get started with plugin/toolshed development for ChimeraX ? Thanks, Florian Wernert

2 1

Measure Motion / Blob Detection
by Scott, Brandon L. 09 Oct '20

09 Oct '20

Hello all, I had two questions: 1) I see there is now the option in measure area to ignore dusted objects, is it possible to have this feature in the measure motion as well? 2) For measure and mark blobs, Is there any way to use the output of the measure motion function to link the blobs since the triangle number changes in each frame, but following measure motion we know where it goes in the next frame. Thanks, Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor Nanoscience & Nanoengineering South Dakota Mines 501 E. Saint Joseph St., Rapid City, SD 57701 724.510.1253 | Brandon.Scott(a)sdsmt.edu<mailto:Brandon.Scott@sdsmt.edu> [South Dakota Mines]<https://www.sdsmt.edu/> [South Dakota Mines on Facebook]<https://www.facebook.com/SouthDakotaMines/>[South Dakota Mines on Instagram]<https://www.instagram.com/southdakotamines/>[South Dakota Mines on Twitter]<https://twitter.com/sdsmt>[South Dakota Mines on Snapchat]<https://www.snapchat.com/add/sdsmt>

2 4

Option Include non-water HETATM in Modeller Comparative
by Marta Martinez 09 Oct '20

09 Oct '20

Hi all, I am running a very simple example in Modeller Comparative (a small alignment including the template structure and the target sequence to model). Since the template harbors a HEME group, I decided to select the Advanced option "Include non-water molecules HETATM residues from template". However, no one of the retrieved models contains the HEME group. Does anyone know what could be happening? Thanks in advance: MARTA -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mmmtnez(a)cnb.csic.es

3 3

right mouse zone selection labels
by Sarah Piper 09 Oct '20

09 Oct '20

HI ChimeraX team, I really like the feature in ChimeraX that creates a map clipping zone in the right mouse tools - zone with automatic labelling. However, the default labels are black background and yellow text, and only the residue 3 letter code and number. Is it possible to change these labels to a white bg and customise the labels to include e.g. the one letter code and chain ID? I tried to do this with the selection - labels tool but it did not seem to change it for the zone labels. Many thanks and keep up the great work :) Sarah

2 2

Error "Cannot determine format for"
by Karjalainen, Mikael 09 Oct '20

09 Oct '20

Hi! I am trying to get transparent background in png pictures, but it is not working and I get error "Cannot determine format for". Only way to get this is by using command line? I am writing something like: save C:\Users\a\Desktop\k [ format png ] [ supersample 4 ] [ transparentBackground true ] or save C:\Users\a\Desktop\k format png supersample 4 transparentBackground true Also, I have tried different variations. Regards, Mikael

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Exporting 3D models from ChimeraX?
by Karjalainen, Mikael 07 Oct '20

07 Oct '20

Hi! Is it possible to export 3D models from ChimeraX? Preferably in formats GLB (best for powerpoint), FBX, OBJ or 3MF? You can in old Chimera, but for powerpoint presentations it can only give STL files which do not have textures. Here are supported file formats for Office products: https://support.microsoft.com/en-us/office/3d-content-guidelines-for-micros… Regards, Mikael

4 10

Request for access to ChimeraX GitHub repository
by Chen, Xiang 05 Oct '20

05 Oct '20

Dear Sir or Madam, I am a graduate student at the Memorial University of Newfoundland, and I am working on the development of virtual reality applications that can be used to visualize biological microscopic data. May I get access to the ChimeraX GitHub repository for further non-commercial research? Looking forward to your reply. Thank you very much! Best Regards, Xiang Chen --- Xiang Chen, Student # 201992538 Department of Computer Science Memorial University of Newfoundland St. John's, NL, Canada T (709) 219-2960 / E xiangc(a)mun.ca

2 1

Access ChimeraX GitHub repository
by 唐翊国 05 Oct '20

05 Oct '20

Hi Dear, I'm learning Python 3 now, and I think one good way is to refer to a good application like ChimeraX, so please allow me to access ChimeraX repository, thanks a lot! BR, Eagle

5 5

orientation
by Fabian Glaser 02 Oct '20

02 Oct '20

Dear chimerax experts, I have maybe a trivial question, I am willing to show a figure with several copies of the same protein, but when I move one copy of them using the "move x 10 model #1” etc command, they rotate upon probably the center of mass of all the models, such as when I separate all of them, they are rotated slightly different. I would like to show them in exactly the same orientation, is there a trick to move them in such a way that will be show in exactly the same orientation? Thanks a lot! Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701 Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ Tel +972 (0) 4 8293701

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ensemble match; ensemble cluster; plotting RMSD
by Cristina Marino Buslje 25 Sep '20

25 Sep '20

Dear ChimeraX users, After a hole evening trying everything, reading every possible page, I can not do what I want that is superposing models of an NMR PDB (ej 20 models) all by all and compare their RMSD (a matrix if possible). And also compare this ensemble (NMR with 20 models) with another (let's say another NMR with 30-50 models). My chimeraX has not the option "Structure comparison" in the tools bars. The web manual doesn't give the commands needed to do so. Below is what is written in the manual but, as I said, structure comparison is not in my tools bar. " Ensemble Match, a tool in the Structure Comparison and MD/Ensemble Analysis categories". I know that there are tools to work with MD simulations (several conformers), but also can not find in the version install in my windows 10 computer. I know this is passible from chimeraX. Could you please help me find the solution? has anybody try this? Is very important for me to do it. Thank you very much in advanced, Cristina Cristina Marino Buslje MS, PhD Researcher, National Research Council (CONICET) Head of Bioinformatics Unit Fundación Instituto Leloir Av. Patricias Argentinas 435. Buenos Aires, Argentina Tel: +54(11)5238-7500 | Fax: +54(11)5238-7501 http://www.leloir.org.ar<http://www.leloir.org.ar/>

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Re: [chimerax-users] [Chimera-users] Is RTX support planned?
by Tom Goddard 25 Sep '20

25 Sep '20

Hi Gökhan, We haven't considered working on raytracing in ChimeraX yet. What advantage do you think it would have? One that I can think of is that having multiples models with transparency could work correctly with raytracing. ChimeraX uses the same material for all surfaces now which defines how light bounces off it, how shiny it is. The ChimeraX material command controls those settings https://www.cgl.ucsf.edu/chimerax/docs/user/commands/material.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/material.html> We may in the future allow different models to use different materials. ChimeraX also allows using textures on surfaces with the "color image" command, although good use cases are hard to come by: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#image <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#image> Generic 3D modeling packages like Blender, Cinema4d, Maya, ... work poorly or not at all with vertex colors which ChimeraX uses for multi-color surfaces like coloring a molecule surface by electrostatic potential. But sometimes people want to export those colorings from ChimeraX, for instance to print a 3D color surface and so they want the colors in a texture. So I have been looking at that use and will probably try to allow electrostatic and hydrophobic coloring to use a texture and to export as GLTF, OBJ, Collada or other 3D formats using texture colors in the next several months. Tom > On Sep 25, 2020, at 1:42 AM, Gokhan Tolun <gokhan(a)uow.edu.au> wrote: > > Hi Tom, > > Are there any plans to implement RTX (real-time ray tracing) support to ChimeraX (and even better, allow the use of physically modelled materials and textures)? > > Thanks, > > Gökhan > > > Gökhan Tolun <https://scholars.uow.edu.au/display/gokhan_tolun>, M.S., Ph.D. > Senior Lecturer > School of Chemistry and Molecular Bioscience <https://www.uow.edu.au/science-medicine-health/schools-entities/school-of-c…> | Faculty of Science, Medicine and Health (SMAH) <https://smah.uow.edu.au/index.html> | Room 125 / Building 18 > Molecular Horizons Research Institute <https://www.uow.edu.au/molecular-horizons/index.html> > Illawarra Health and Medical Research Institute <https://www.ihmri.org.au/researchers/gokhan-tolun/> > University of Wollongong NSW 2522 Australia > T +61 2 4221 3365 > uow.edu.au <http://uow.edu.au/> | Facebook <https://www.facebook.com/UOW> | Twitter <https://twitter.com/uow> | Instagram <https://www.instagram.com/uow/> | LinkedIn <http://www.linkedin.com/edu/school?id=10255> > > NOTICE: This email is intended for the addressee name and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Please consider the environment before printing this email. > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

1 0

Center of cube in mrc
by Luis José Castillo Valverde 24 Sep '20

24 Sep '20

Hello, I want to move a mrc near another mrc from terminal controlled, the problem is that I don't know how ChimeraX defines the center point of movement when loading a mrc file. So I wanted to know if you can explain to me that ChimeraX defines the X, Y, Z coordinates in which it will load the center of the cube? Best regards, Luis -- Luis José Castillo Valverde Ingeniero en Computación, TEC Costa Rica Estudiante de maestría (MSc) académica en Computación, TEC Costa Rica Telegram: @LCastillo98 LinkedIn: luisjosecastillo98

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Re: [chimerax-users] Exporting image in 300 DPI
by Fabian Glaser 22 Sep '20

22 Sep '20

Dear all, I saw Elaine mail regarding the 300 DPI question, but I am not able to get more than 72, I played with the width and heigh as follows: save /Users/fglaser/test2.tiff pixelsize 0.1 save /Users/fglaser/test2.tiff width 900 But I am not able to get more than 72. Could you please help me to get 300 DPI? Thanks! Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701 Elaine Meng meng at cgl.ucsf.edu <mailto:chimerax-users%40cgl.ucsf.edu?Subject=Re:%20Re%3A%20%5Bchimerax-users%5D%20Exporting%20image%20in%20300%20DPI&In-Reply-To=%3C439F4072-9421-4196-8095-5824C8FB5DB4%40cgl.ucsf.edu%3E> Tue Jan 21 08:17:48 PST 2020 Previous message: [chimerax-users] Exporting image in 300 DPI <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/000813.html> Next message: [chimerax-users] silhouettes on mesh in ChimeraX <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/000819.html> Messages sorted by: [ date ] <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/date.html#816> [ thread ] <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/thread.html#…> [ subject ] <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/subject.html…> [ author ] <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/author.html#…> Hi Ahmed, Currently the saving dialog does not show many options, but the “save” command includes all of these controls. Use the “save” command with “width” and/or “height” option, where the values are numbers of pixels. You would just calculate the pixels by multiplying the desired size in inches by the dpi. E.g. 3 inches wide X 300 dpi = 900 pixels wide. See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image>> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Keep mouse or pointer active in recorded movies
by Sarah Piper 21 Sep '20

21 Sep '20

Hi ChimeraX team, I was wondering whether there is an option to make a mouse/cursor (or some sort of other pointer) visible when movies are recorded? E.g. When I want to point to my model or run simulations in Isolde and move atoms around, my mouse/cursor is not visible in the recording. Is it possible to keep the cursor visible in the recording, so that it becomes clear what was moved/pointed at in a movie recording? I hope the question make sense! Many thanks for all your work on this, awesome piece of software! Regards, Sarah

3 3

best desk-top for Chimerax
by Homer Guy 21 Sep '20

21 Sep '20

What are the best desk-tops for Chimerax using Windows 10 64 bit? H. Robert Guy

2 1

Registration of ChimeraX
by Raymond P. Cox 19 Sep '20

19 Sep '20

I would like to register ChimeraX but I cannot enter @ in the box for my email address. Instead, the @ appears on the command line. Best regards Raymond Cox University of Southern Denmark

2 1

Hiding pivot in ChimeraX
by Mutum Yaikhomba 18 Sep '20

18 Sep '20

Hi Is there a way to hide the pivot in ChimeraX? The pivot automatically appeared when I started ISOLDE in ChimeraX. Screenshot of the pivot attached. I looked on how to hide this pivot up online - but could not find it. Thanks Yaikhomba

2 3

Fwd: Unable to load --offscreen and --nogui options
by Sai Janani Ganesan 15 Sep '20

15 Sep '20

Hello All, I am unable to save images from the command line, I get an OpenGL error. I get openGL errors on both Mac and Linux. Any suggestions? ChimeraX --offscreen --nogui test.cxc Traceback (most recent call last): File "/opt/chimerax-1.0-1.fc32/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/opt/chimerax-1.0-1.fc32/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/ChimeraX_main.py", line 895, in <module> exit_code = init(sys.argv) File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/ChimeraX_main.py", line 453, in init sess = session.Session(app_name, debug=opts.debug, silent=opts.silent) File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/chimerax/core/session.py", line 441, in __init__ self.logger = logger.Logger(self) File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/chimerax/core/session.py", line 501, in __setattr__ if not name.startswith('_') and self.snapshot_methods(value, base_type=StateManager) is not None: File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/chimerax/core/session.py", line 535, in snapshot_methods from chimerax import graphics as gr File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/chimerax/graphics/__init__.py", line 34, in <module> from .opengl import Texture, Lighting, Material File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/chimerax/graphics/opengl.py", line 61, in <module> from OpenGL import GL File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/GL/__init__.py", line 4, in <module> from OpenGL.GL.VERSION.GL_1_1 import * File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/GL/VERSION/GL_1_1.py", line 14, in <module> from OpenGL.raw.GL.VERSION.GL_1_1 import * File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/raw/GL/VERSION/GL_1_1.py", line 7, in <module> from OpenGL.raw.GL import _errors File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/raw/GL/_errors.py", line 4, in <module> _error_checker = _ErrorChecker( _p, _p.GL.glGetError ) AttributeError: 'NoneType' object has no attribute 'glGetError'-- Thanks, Sai

3 3

Loading OpenMM platform plugins
by Thomas Mulvaney 15 Sep '20

15 Sep '20

Hi, I've been having fun developing a plugin for ChimeraX and want to firstly thank everyone involved for such a great platform to build upon. I'm starting to introduce a molecular dynamics component and was excited to see that ChimeraX ships with OpenMM support. Unfortunately, the OpenMM Platform plugins (which add CPU, CUDA, OpenCL etc) functionality, do not seem to be loaded by default at least in ChimeraX 1.1 on macOS. I couldn't see any documentation about how to load these plugins, but for anyone running into this issue, the following code got things working for me: ------ import chimerax openmm_plugins_dir = os.path.join(chimerax.app_lib_dir, 'plugins') Platform.loadPluginsFromDirectory(openmm_plugins_dir) ------ Kind regards, Tom

2 2

headless chimerax is built in via --offscreen and --nogui
by Moth, Christopher W 14 Sep '20

14 Sep '20

For other longtime and unimaginative 🙂 legacy chimera users who might be googling/searching for 'headless chimerax', hopefully this note will be picked up by search engines The details you seek: http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-April/000472.html No need to reply.

1 0

Choosing solvent exposed residues automatically
by Mutum Yaikhomba 09 Sep '20

09 Sep '20

Hi I am working with a very big pdb model: pdb - 6g2j. I was wondering if there is a quick way to select all residues (surface residues) that are exposed to the solvent (including those facing the membrane)? This is instead of going over each residue one by one and selecting them. Additionally, say you have selected these solvent-exposed residues and now you want to filter them based on Hydrophobicity - is there a way to filter based on the standard Kyte-Doolittle Hydrophobicity index for these residues? If there is, it would be of great help and very much appreciated. Thanks Yaikhomba

2 3

mousemode and ISOLDE
by Alexis Rohou 06 Sep '20

06 Sep '20

Hi all, Not sure whether this is a ChimeraX question, or an ISOLDE question, or a bit of both. I am using ChimeraX 1.0 (2020-06-04) and ISOLDE version ChimeraX_ISOLDE-1.0.1-cp37-cp37m-macosx_10_13_x86_64.whl. When I start ChimeraX, I get the following left mouse bindings, which I believe are default: - ctrl-left click = select - shift-ctrl-left click = select add When I just start ISOLDE via the GUI menu (no further action), this seems to clear the mousemode. Or, at least, ctrl-click does not select anymore, and shift-ctrl-click also doesn't seem to do anything. To remedy this, I issue the following commands: mousemode control left select mousemode control shift left 'select add' This restores ctrl-left to 'select' as expected, but shift-ctrl-left also triggers 'select', not 'select add'. Couple of questions: (1) Is ISOLDE intentionally overriding mousemode when it is launched? I'm 99.9% this didn't use to be the case pre-1.0... (2) How do I restore shift-ctrl-left to 'select add'? I assume I am getting the syntax wrong, but I did read the doc and thought I was following it, so I guess I need some help understanding the syntax. Cheers, Alexis

3 3

Fit Map Question/Articles
by Luis José Castillo Valverde 03 Sep '20

03 Sep '20

Hello, I am currently working on my thesis work (this is why they have received many questions from me these days), this is why I am collecting information on biomolecular structures, and I wanted to know if you know of any article that comments on the pros and cons of its "Fit Map in Map" algorithm? This because I have been searching on this topic and have not been able to find anything. Sorry for the inconvenience and thanks in advance. Best regards, Luis -- Luis José Castillo Valverde Ingeniero en Computación, TEC Costa Rica Estudiante de maestría (MSc) académica en Computación, TEC Costa Rica Telegram: @LCastillo98 LinkedIn: luisjosecastillo98

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Re: [chimerax-users] [Chimera-users] User-defined graphics in chimera: NMR tensor plotting
by Tom Goddard 31 Aug '20

31 Aug '20

Hi Albert, Not sure if you are talking about using a modified version that spherical Python code in Chimera or using it in ChimeraX. I'll assume ChimeraX. http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics <http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics> It is much easier to shift and rotate the vertices than your approach. Python numpy arrays make this very convenient. After the line of code that makes the numpy array of vertices va = array(vertices, float32) you could shift it to a new origin with just va += (32.5, 13, -24.1) Rotation is also easy. from chimerax.geometry import rotation r = rotation(axis = (0,1,0), angle = 45) va = r * va na = r * na Here I rotate the vertices and the normal vectors about 0,0,0. Then I could apply the translation after that. You might want to do a rotation given by a 3 by 3 rotation matrix and the translation in one step, like this from chimerax.geometry import Place t = Place(matrix = ((0,1,0, 32.5), (-1,0,0, 13), (0,0,1, -24.1))) t.transform_points(va, in_place = True) t.transform_vectors(na, in_place = True) Here I used a 3 by 4 matrix where the first 3 columns were the rotation and the 4th column is the translation. I'll update the example code to show this. These geometric transforms are described in the ChimeraX Python programming documentation: https://www.cgl.ucsf.edu/chimerax/docs/devel/bundles/geometry/src/geometry.… As for what went wrong with you np.array([x0,y0,z0]).T approach -- that transpose operation put the vertices in a non-standard memory order -- you created a 3 by N array and then did a transpose to get an N by 3 array but numpy is smart and does not allocate a new array and instead just adjusts the strides and uses the original array. My guess is the calculate_surface_normals() code has a bug in that it does not handle non-standard orders for the vertex array. So the normals were completely wrong and that effects the lighting. In the ChimeraX Python shell (menu Tools / General / Shell) the variable "session" is the ChimeraX session. Tom > On Aug 31, 2020, at 2:43 PM, Albert Smith-Penzel <Albert.Smith-Penzel(a)medizin.uni-leipzig.de> wrote: > > Dear all, > > Thanks for such quick replies and helpful answers. I had two follow-up questions on the approach that Tom suggested in ChimeraX. > > The first is maybe a glitch, or more likely something I don’t fully understand in python/chimera. > > In the code Tom links to (http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics <http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics>), a list of vertices (x,y,z tuples) is created. Suppose I want to shift the center of the spherical harmonic and/or rotate it. One way to do this is to extract x,y,z from the vertices list and modify them, then put them back in the list. My first step is to switch the tuple to a list in the code (switch xyz = (r*sp*ct, r*sp*st, r*cp) to xyz = [r*sp*ct, r*sp*st, r*cp] ). Then I extract the elements, do some editing, and then put them back into a list of vertices. > > x0,y0,z0=np.array(vertices).T > #Some editing of x0,y0,z0 - although editing is not required to produce the strange effects. > vertices=np.array([[x,y,z] for x,y,z in zip(x0,y0,z0)]) > #vertices=np.array([x0,y0,z0]).T > > Finally, I need to reconstruct the vertices list. The first approach (currently uncommented) works just fine. The second approach (commented) doesn’t create any errors, but the lighting is very strange, in that there are alternating dark and light areas on the surface of the harmonic. I would have claimed that the two approaches should produce practically identical numpy arrays, but clearly that’s not the case. > > Anyway, it’s not particularly important for me, since I can work around it, but it does take some time to figure out, because one would think the latter approach should also work. > > The second question is: is it possible to get the “session” object into an interactive python session? Usually, I work interactively with python, and have a number of functions that create various scripts and input files for chimera, and then launch chimera from a shell, calling some script on startup. While this works, it would be really nice if one could manipulate an existing chimera session (maybe a bit off of the original topic now). > > In any case, the new graphics with the tensors come out very nicely- thanks so much for your help. > > Cheers, > Albert > > > >> On 28. Aug 2020, at 20:58, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> WARNUNG: Diese E-Mail kam von außerhalb der Organisation. Klicken Sie nicht auf Links oder öffnen Sie keine Anhänge, es sei denn, Sie kennen den Absender und wissen, dass der Inhalt sicher ist. >> >> Hi Albert, >> >> You need finer phi and theta steps to get a smoother appearance. I found that 10 degree steps gives chunky appearance, while 3 degree steps givs smooth appearance. Chimera does not have code to make an arbitrary surface smoother. >> >> Maybe you are interested in making these surfaces all in Python instead of using BILD. Here is how it is done in our newer ChimeraX program. >> >> http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics <http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics> >> >> Tom >> >> <harmonics.png> >> >>> On Aug 28, 2020, at 1:54 AM, Albert Smith-Penzel <Albert.Smith-Penzel(a)medizin.uni-leipzig.de <mailto:Albert.Smith-Penzel@medizin.uni-leipzig.de>> wrote: >>> >>> Hello, >>> >>> I have a question about improving user defined graphics in Chimera. >>> >>> For background (maybe not necessary for answering): >>> I’m working with nuclear magnetic resonance and MD simulation, and so I want to plot dynamically averaged spin-spin (H–C) dipole tensors, obtained from MD, on top of the corresponding H–C bonds. I’ve been relatively successful, but while one has a very high-resolution picture of the molecule itself, the tensors themselves are visibly triangulated. >>> >>> How I get this plot: >>> Each tensor is expressed first in spherical coordinate (theta, phi, r). In python, I run Delauney from scipy.spatial on theta and phi to get a list of vertices that can be used for triangulation of the tensor. Then, for each tensor, I convert theta, phi, and r into cartesian coordinates, shift the center so that the tensor sits on top of the correct bond. Finally, I create a .bild file where I write out each triangle using the coordinates and vertices. Tensors have negative and positive values (red and blue in the plot), and so I only take triangles for which r for all vertices is positive, and then in a second step, take only triangles where all vertices are negative. This all gets written to the .bild file, and then opened in chimera on top of the molecule (see picture). >>> >>> The question: >>> The result is certainly acceptable, however, there is clearly a quality difference in the molecule rendering vs. the tensor rendering (obviously, because the tensors are just made of triangles that I’ve created in python). Is there a better way to bring the surface data describing the tensors into chimera that would then allow usage of some sort of smoothing within chimera for a nicer image? (And possibly with a relatively simple data format….) >>> >>> Thanks for your help! >>> >>> Cheers, >>> Albert Smith >>> >>> <example_triangulation.png> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> >> > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

1 0

Fit in Map - Overlap
by Luis José Castillo Valverde 28 Aug '20

28 Aug '20

Hi, As I understand it, the overlay resulting from the "Fit in Map" command corresponds to the sum over the fit map grid points of the product of the fit map value and the reference map value at that point, determined by trilinear interpolation. I want to calculate the percentage of overlap of two maps, it would be as simple as calculating the formula "min ((sum of the grid points of map 1), (sum of the grid points of map 2)) / (overlap obtained from the fit ) "the problem I have that I do not know how to obtain those values (" sum of the grid points of map 1 "," sum of the grid points of map 2 "); I tried to do "Fit in Map" of map 1 with map 1 and use the overlap that returns as the sum of the points of map 1 but it didn't work. So I wanted to know if you can tell me how to get the sum of the grid points of a given map. Regards, Luis -- Luis José Castillo Valverde Ingeniero en Computación, TEC Costa Rica Estudiante de maestría (MSc) académica en Computación, TEC Costa Rica Telegram: @LCastillo98 LinkedIn: luisjosecastillo98

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MD trajectories in ChimeraX
by David Slochower 24 Aug '20

24 Aug '20

Hi, are there any plans to implement a "metafile" interface (e.g., http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#…) for loading trajectories with ChimeraX? In particular, it would be great to be able to load `prmtop` and `nc` trajectories, even if it were available only through the command line and without a GUI. (This can be considered a follow up to this message: http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-December/000773.html) I'm aware of the Molecular Dynamics Viewer in the Toolshed, but that appears to be geared for multi-PDB trajectories. Thanks.

2 3

Stack sidebar tools as tabs
by Sean Connell 22 Aug '20

22 Aug '20

Hello, I was wondering if there is a command to automatically stack the tools (i.e. log, volume viewer) in the sidebar as TABs? For example to put in the preferences so it starts this way or to make an alias so it can be done quickly. Thanks in advance for any tips you have. Sean

2 1

ChimeraX depthCue
by Gokhan Tolun 18 Aug '20

18 Aug '20

Hi, Based on here: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html I am trying to adjust the depth cue using the depthCue true | false depthCueColor color-spec depthCueStart start depthCueEnd end commands, but I get the error Unknown command: Any suggestions? Thanks, Gökhan PS: ChimeraX 1.0

2 2

Oculus quest for chimeraX?
by Miriam Díaz Galicia 18 Aug '20

18 Aug '20

Dear chimeraX users I would like to buy my first VR headset to use with ChimeraX. I am considering buying the Oculus quest but I would like to confirm that it will properly work for ChimeraX. Has anyone used it? or is there a better low-cost VR headset (preferably but not limited to all-in-one devices) that you can recommend to me? Thank you very much in advance, Escarlet -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

3 8

Draw a circle
by Andrea Dallapè 18 Aug '20

18 Aug '20

Hi, I would like to highlight a hole in a protein -the exit tunnel of a ribosome, to be more specific. I tried the command shape tube in order to draw three tubes passing through three residues, but the result doesn't suit at best my need and expectations. Is possible to draw a circle, passing through three points -or residues-? Do you have any suggestions? Thank you for your attention. Have a great week end. Greetings, Andrea

2 5

Re: [chimerax-users] [Chimera-users] [External] Re: The command like volume zone in X
by Tom Goddard 14 Aug '20

14 Aug '20

Hi Fengwei, I added the "wobble" command to ChimeraX today that makes a figure 8 motion. It will be in tonight's ChimeraX builds -- nightly builds are listed at the bottom of the downloads web page. The wobble command is just a shorthand for the turn command and the turn command now has two new options: wobble that controls speed and is the number of frames for a complete figure 8, and wobbleAspect that controls the amplitude of the bobbing motion as a fraction of the side to side motion (default 0.3). The wobble command uses a default cycle of 136 frames per second which at 60 frames/second rendering is a little more than 2 seconds per figure 8. The wobble command makes the default amplitude 15 degrees. Tom > On Aug 14, 2020, at 9:37 AM, Zheng, Fengwei wrote: > > Dear Elaine, > > Got it, Thank you so much for your kind explanation! Stay safe and Have a great weekend! > > Best, > Fengwei > From: Elaine Meng > Sent: Friday, August 14, 2020 12:34 > To: Zheng, Fengwei > Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> > Subject: [External] Re: [Chimera-users] The command like volume zone in X > > Hi Fengwei, > There is a "vop zone" command in Chimera similar to "volume zone" in ChimeraX. Same function, but the keywords and syntax are different, see > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone>> > > E.g. something like: > > vop zone #2 #0:.a 2 > > As for your other question, Chimera has a "precessionTilt" option to the "roll" command, but ChimeraX does not have this option currently. Looking at this kind of motion makes me feel seasick, so I don't use it in my own work. > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/roll.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/roll.html>> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Aug 14, 2020, at 8:43 AM, Zheng, Fengwei wrote: > > > > Dear Developer, > > I am wodering if there is a command of Chimera can achieve the same function like "volume zone" in ChimeraX? I tried the command "vol zone #2 near #0:.a range 2", but the chimera always said "unknow keyword #2"~ > > Another thing is that I wonder if there is a command of ChimeraX can achieve the same function like "turn z 2 360 precess 20" in Chimera (to achieve the Wobble motion / "wiggle-rock" motion, like nutation in pymol)~ > > The I tried 1.14, 1.15 and the latest daily built versions of Chimera. > > The ChimeraX version I used is 1.0, Many thanks! > > Best, > > Fengwei > > CAUTION: This email was sent from outside of the organization (meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>). Do not click links or open attachments unless you recognize the sender and know the content is safe. If you have any questions, please contact ServiceDesk(a)vai.org <mailto:ServiceDesk@vai.org> <mailto:servicedesk@vai.org <mailto:servicedesk@vai.org>>. > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

2 1

Discrete coloring and secondary structure assignment.
by Reza Khayat 13 Aug '20

13 Aug '20

Hi, I'm trying to generate a ribbons diagram where the secondary structures are defined by user and colored by user. I'm running into a problem where half of the amino acid is assigned the secondary structure and the entire residue is assigned the color. This makes for a strange image. Attached is an image. Notice how the coloring starts before the secondary structure. Any help is appreciated.? Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

2 4

Limits on movies
by mailman-bounces＠cgl.ucsf.edu 13 Aug '20

13 Aug '20

From: Maria Maldonado <mmaldo(a)ucdavis.edu <mailto:mmaldo@ucdavis.edu>> Subject: Limits on movies Date: August 9, 2020 at 7:23:21 PM PDT Hi! I have a question about movies and thought you might be able to help. Is there a limit to the length of the movies other than the limit maxframes? I’ve made scripts for movies with several steps. All the motions/commands show in the ChimeraX window while it is rendering, the script gets to the end and says “movie encoded”. However, when I open the movie file, the movie is missing several frames/steps. This happens even though I increased the limit maxframes (and my movies should be shorter than 15000 to begin with). If I split the original movie into shorter chunks that works fine, but I’ll have to edit the steps together in a different programme. I was wondering if this has to do with ChimeraX, or whether maybe it could be a computer memory issue or something else outside of the programme? It seems to be worse (ie the movie file stops earlier) for larger volumes and models than for smaller ones. Thank you very much for your help! Best, Maria

4 6

chimerax amino acid sequence
by Peter Steinhagen 09 Aug '20

09 Aug '20

Hello, I am new to chimerax. For my protein of interest, there is no PDB available, thus, I chose a similar protein. However, the amino acid sequence is different. Is it possible to change the amino acid structure in chimerax? Will this change the 3D conformation? If this does not work what would be a good solution for my problem? Thanks, Peter

2 2

Command line utility for .cmap
by Daniel Asarnow 06 Aug '20

06 Aug '20

Hi all, I have only been able to load volume series data using the .cmap format (using a daily from this week on OS X). Is there a command-line utility, perhaps ChimeraX itself, that can generate a .cmap file from a number .mrc volumes? It would be nice to generate these on my processing machine and then only download the .cmaps to my laptop. Best, -da

4 6

Server maintenance
by Eric Pettersen 06 Aug '20

06 Aug '20

Hi all, The servers that usually host the Chimera web site and web services will be undergoing maintenance Monday and Tuesday of next week (August 10/11), but we have jury-rigged a temporary solution that should allow the web site and services to continue to function through the maintenance window. Nonetheless, do not be shocked if the site/services wind up being down on those days. Also, mail to the Chimera mailing lists and Chimera bug reports will be not be fully processed until the servers fully come back up on Wednesday. Such mail/reports will be accepted but spooled during the maintenance window, and delivered afterward. So you probably will not get any responses until Wednesday/Thursday. --Eric Eric Pettersen UCSF Computer Graphics Lab

1 1

ChimeraX Toolshed will be down 10-11 August 2020
by Greg Couch 05 Aug '20

05 Aug '20

Hello everyone, The ChimeraX Toolshed will be down for two days starting Monday, August 10th, 2020. This is due to a major infrastructure upgrade. We are planning to keep the regular ChimeraX web site up during that time, but there's a small chance that it will be down too. Everything should be back to normal by Wednesday, August 13th. If not, we will be frantically working on getting it back up :-). -- Greg

1 1

Fit map in map and save result map
by Luis José Castillo Valverde 05 Aug '20

05 Aug '20

Hello, I know that the ones I am going to ask maybe a recurring question but I have not managed to solve it. I know that maps as such do not have location or rotation information, but I want to generate a new map (with a new cube I imagine) which represents the current position and rotation for a given map. I am working with "fitmap (map # 1) inmap (map # 2)" the idea is to generate the new map from the optimized map, to be able to load that new "result" map without the need to perform any other transformation. If this is possible, I wanted to know if you can give me the command list to be able to do it? I already appreciate the attention provided. Best regards, Luis -- Luis José Castillo Valverde Ingeniero en Computación, TEC Costa Rica Estudiante de maestría (MSc) académica en Computación, TEC Costa Rica Telegram: @LCastillo98 LinkedIn: luisjosecastillo98

2 2

OpenGL error with nogui?
by Fabian Glaser 01 Aug '20

01 Aug '20

Dear gurus, I am trying to produce a series of figures on the fly with chimeraX, using a python script of the following format (this is only a simple demo): test.py: #!/usr/bin/env python3 import sys from chimerax.core.commands import run run(session, "open 1d66") run(session, "color red") run (session, "save fig1.png”) == This works like a charm with the gui, but without the gui it gives the following error, stops and no figure is produced, we tried both in Mac and linux. We are interest in the —nogui option: .../MacOS/ChimeraX --script "test.py 1d66" —nogui Executing: surface sel-residues enclose sel-residues Executing: transparency 0 ribbons Set transparency of 542 residues Executing: ~select Nothing selected Nothing selected Executing: save fig1.jpg Unable to save images because OpenGL rendering is not available So is this solvable? How? We tried also with the —offscreen, no luck either. Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ Tel +972 (0) 4 8293701

2 1

command: symmetry, option: contact
by Roberto Marabini 31 Jul '20

31 Jul '20

Dear all, In chimera I used to use the command sym #0 group i,222r contact 3 to surround an asymmetric unit cell by its neighbors. I see that, in chimerax, "sym" no longer has the option "contact" (or the alternative option "range"). Is there any way to get results similar to the ones obtained using chiera command sym #0 group i,222r contact 3 with chimerax

4 4

Cartoon and ribbon display - change atoms for nucleic acid from C5' to Phosphate
by bertrand beckert 31 Jul '20

31 Jul '20

Dear ChimeraX developper, I was wondering if in ChimeraX it is possible to change the atoms used for the cartoon/ribbon display. According to the online user manual ( https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#top) for the nucleic acid the cartoon path seems to be restricted and guided by only the C5'.... could it be possible to change the C5' to the Phosphate instead? is there already a command existing ? Thanks for the nice software! Best regards Bertrand

2 1

Re: [chimerax-users] ChimeraX command line iterate through models for individual file export
by Tom Goddard 30 Jul '20

30 Jul '20

Hi Austin, Of course I remember you, it was a great trip to Rocky Mountain Laboratories. Thanks for your hospitality! And I see your SARS-Cov-2 images in the media -- very nice. Here's the ChimeraX voodoo to save all your objs in one command perframe "save ~/Desktop/objs/model$1.obj model #1.$1" frames 23 It uses the perframe command that runs another command once each frame (usually used for recording an animation video). The $1 gets the frame number substituted in 1, 2, 3 and the frames tells it how many frames, in your case use 100 to get the 100 models. Here are the perframe docs https://www.cgl.ucsf.edu/chimerax/docs/user/commands/perframe.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/perframe.html> if you need more info. Tom > On Jul 29, 2020, at 10:19 PM, Athman, Austin (NIH/NIAID) [E] <austin.athman(a)nih.gov> wrote: > > Tom, > > I’m Austin Athman, from the NIAID Rocky Mountain Laboratories Visual Arts Department. I took some of your sessions on ChimeraX when you were out to Hamilton MT in the past, and I believe you assisted my colleague Ryan Kissinger on some ChimeraX questions he had. I have one for you I hope you can help. > > I have received a morphing model of the spike protein on RSV for an animation project we are working on for Barney Graham and Jason McLellan. The morph is in 100 steps, and I have 2 different morphs (one for attachment, and another for fusion), making 200 steps total. I am exporting the surface model of each step to an OBJ file for use in our animation software. I have managed to write a single command line that I copy/paste in over and over, changing just the id and file number for export to get the files I need. > > Is there a way I can automate this further, so that ChimeraX will iterate through each id and export to individual files for me without copy/pasting the command each time and modifying it? It would save me hours of time. > > Unfortunately, I am very new to ChimeraX, and know only enough to get me into trouble, specifically, how to show/hide surfaces, and export! > > Here is a screenshot of my model, and also the Excel doc I use to keep track and build my command for each file export, just so you can see what I am doing at the moment. It takes some time for each to save as well, so I don’t know if that delay will make it difficult for the command line to wait and continue each time for each export. There may be some additional commands I can just add between each line in the excel, and I can just copy and past the entire thing and let it run, but that is where I hope you might be able to tell me what I am missing. > > Hope you are well in these times. Also, thank you for your work and videos on coronavirus. Good informative stuff. > > -Austin Athman > > > > <image006.jpg> > > <image008.jpg> > > > > > -- > <image009.png> > ..................................................................... > Rocky Mountain Laboratories NIH/NIAID > Research Technologies Branch <http://myrtb.nih.gov/> > 903 South 4th Street > Hamilton MT 59840 > Phone: (406) 375-7480 > > DISCLAIMER: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

1 0

source code of ChimeraX
by Сергій Кущ 29 Jul '20

29 Jul '20

Hello! How to download source code of ChimeraX?

2 1

VOP cover command?
by Megan Mayer 29 Jul '20

29 Jul '20

Hi chimeraX forum, I am trying to get an electron density map (.mrc) to overlap with atomic structure (.cif) file of a small organic molecule. When I open my electron density map in ChimeraX, only one rectangle ( i am assuming one lattice piece) appears, which does not encapsulate the entire small molecule. I am thinking to use the "vop cover" command to get the density to expand to multiple lattices, but I am not sure what numbers to enter. When I try "vop cover atomBox #2" (#2 is the ID of the .cif structure), I get a "Missing or invalid 'volumes' argument: invalid density map specifier" response. Thanks in advance for any help!! Megan

2 6

Can I get atomic coordinates from an electron density map in xplor format via ChimeraX software?
by 王超 28 Jul '20

28 Jul '20

3 2

Interfaces
by Reza Khayat 27 Jul '20

27 Jul '20

?Hi, Is it possible to save the image generated with residue plot from command interfaces? I can use screen capture to do this, but an internal save would keep the images a constant size. Thanks. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

2 2

Clip surface but not atoms
by Pufall, Miles A 27 Jul '20

27 Jul '20

Hi! I’ve used Chimera for years (though not recently) and am switching to ChimeraX. I’m looking to display the ligand binding pocket with the ligand, and the tutorial you have is great. I generated this picture, which is really close to what I want. It shows the ligand, and the pocket, and I’m able to slice it with the interactive side view tool to get to this point. However, the left side of the ligand is slightly clipped. I’ve played with rotation and with moving the slice plane, but can’t find an orientation that shows the pocket so nicely (without any surface in the foreground) and not ligand clipping. My question is: is there a way to tell ChimeraX to clip the surface but not the ligand? Thanks! Miles [cid:9F2E9E3C-2209-4033-98F8-C1726F0DFD85@dynamic.uiowa.edu] ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

3 9

Alternate locations
by Jeschke Gunnar 27 Jul '20

27 Jul '20

Hi ChimeraX team, very nice program and remote control scheme! Clear thinking, cool implementation. My question/suggestion is about alternate atom locations. ChimeraX knows about them. I load 1lcd info atoms /A:8@NE2 attribute alt_locs correctly responds: atom id /A:8@NE2 alt_locs A,B When I show /A:8@NE2 or I show /A:8 as sticks, only location A is displayed. When I retrieve atom coordinates, only location A is returned. Could you implement full handling of alternate locations (or am I doing something wrong here? I really tried a lot to find location B). Kind regards Gunnar --- Der Schlaf der Vernunft gebiert Ungeheuer - Francisco Goya Prof. Dr. Gunnar Jeschke ETH Zurich Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 2 CH-8093 Zurich Switzerland www.epr.ethz.ch

2 4

surface colouring by selected residues
by Oleksiy Kovtun 27 Jul '20

27 Jul '20

Dear ChimeraX community, I need to colour the surface by selected side chains to highlight an intermolecular contact. The command sequence: #select atoms on the buried surface. The selection works correctly: measure buriedarea #10/C:449-end withAtoms2 #9/A:449-end select true #make a surface. A new surface #10.1 is generated: surface #10/C resolution 7 #color surface yellow at selected residues. color #10 & sel yellow target s The last command does not result in surface colouring although reports "colored 1 surfaces" upon its execution. Where is a mistake in the colouring approach? I run chimeraX version 1.0 (2020-06-04) on Ubuntu 18.04. Thank you and best regards. Oleksiy Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun(a)mrc-lmb.cam.ac.uk

3 4

Cleanest Way to Install Daily Build
by Anderson, Jacob 24 Jul '20

24 Jul '20

Just wanted to reach out to see if there is a clean way to replace one's current ChimeraX with the daily-build (specifically Ubuntu). Is it best to uninstall/the prior and just install the desired version? Thank you for any thoughts! ~jacob

2 1

CryoET map problems
by Andrea Dallapè 21 Jul '20

21 Jul '20

Hi, I have an EM map -from a cryoET experiment- and I would like to use ChimeraX in order to fit the protein -the ribosome, in this case- in such EM map. I don't understand why the PDB of the ribosome I open in ChimeraX is far bigger than the EM map I have, and I don't really know how to resize them in order to have a fittable model. Could you suggest me a solution? Thank you for your help and attention, Andrea

2 1

How to set RGB color for user selected atoms?
by Donovan Chin 17 Jul '20

17 Jul '20

Hi How do i set RGB colors for user-selected atoms? Or for custom atom selections? Cmd line? Regards -D Donovan Chin | Director of Computational Drug Discovery | +1 617 899 5333 | dchin(a)arrakistx.com<mailto:dchin@arrakistx.com> Disclaimer The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful. This email has been scanned for viruses and malware.

2 1

Bond between two sequential residues
by Derek Harris 17 Jul '20

17 Jul '20

Hello, When I hide the backbone and choose to show side chain and base any sequential residues shown have a small line between the CA's. I can select them, but not delete them or hide them as an atom or bond, only hide sel, but when the selection they are a part of is hidden and reshown they reappear. I can also assign them as a selector and hide/show them, but also as soon as I hide and reshow the selection they are a part of they reappear and the designated selector for them is gone from the list. I want to retain the side chain and base appearance but lose these lines permanently. Any help would be appreciated. Derek Harris Postdoctoral Fellow Seefeldt Lab Department of Chemistry and Biochemistry Utah State University

3 5

About "color by RMSD "
by Dr.Jason 17 Jul '20

17 Jul '20

Dear Chiemra X team: Briefly, I want to ask you how to color a protein structure by RMSD in chimera X, after done matchmaker of two structures ? I know chimera can do this job, but I did’t find the equivalent function in chimera X. Allen Wu Allenwu1991(a)163.com Chengdu. China

2 2

Re: [chimerax-users] Using Vive controllers with webcam function in ChimeraX
by Tom Goddard 15 Jul '20

15 Jul '20

Hi Józef, The Vive controllers only work in VR mode. You could enable VR mode and just not put on the headset. The "vr roomCamera" command would allow showing the molecular graphics in the desktop window from a specific position which you would want to match your webcam's physical position in the VR space. And you will want to match the vr roomCamera field of view to the field of view of the webcam. Then you will have several problems. First, the hand controller cones won't line up perfectly with the video of the hand controllers -- there will be unpleasant lag. And without the VR headset on it will be very challenging to point at things. But you might as well put on the VR headset to solve that. Then it should work -- you can use the VR with webcam AR. This is just what I did with VR plus a depth sensing camera except that the depth camera also can blend the depth correctly. Tom > On Jul 15, 2020, at 12:22 PM, Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk <mailto:J.R.Lewandowski@warwick.ac.uk>> wrote: > > Hi Tom, > > Would it be possible to use Vive controllers without going into the vr mode but rather during the webcam session? > > Thanks, > Józef > > ------------------------------------------------------------------------------------------------------ > Józef R. Lewandowski > Professor | Department of Chemistry | University of Warwick <http://www2.warwick.ac.uk/> > j.r.lewandowski(a)warwick.ac.uk <mailto:j.r.lewandowski@warwick.ac.uk> | External: +44 (0) 24 76151355 | Internal: 51355 > Millburn House: F07 | Coventry CV4 7AL | Find us on the interactive map <http://www2.warwick.ac.uk/about/visiting/maps/interactive/> > Lewandowski group website <https://www2.warwick.ac.uk/fac/sci/chemistry/research/lewandowski/lewandows…> | Warwick solid-state NMR group website <http://www2.warwick.ac.uk/fac/sci/physics/research/condensedmatt/nmr/>

1 0

Non existent attributes default to all objects
by Daniel Esteban Palma Igor 15 Jul '20

15 Jul '20

Hi, if in a command you use an attribute that does not exist, ChimeraX (1.0) uses all the objects, for example: show @@asdf Is this intended? Regards, Daniel Palma Igor

2 1

Color electrostatic ValueError
by Maria Maldonado 14 Jul '20

14 Jul '20

Hello ChimeraX team, I was hoping you could help me with a python error I get when trying to use the color electrostatic command. I have my protein surface and my electrostatic map from Delphi in cube format. When I run “color electrostatic #1 map #2 palette -10,red:0,white:10,blue”, I get long error ending in “ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() File "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/gaussian/gaussian_format.py", line 120, in matrix if self.matrices == None: See log for complete Python traceback.” (I can send you the full error if useful.) I don’t get the error if I use a Delphi .phi file. However, the .phi files from this Delphi version have a bug that distorts the map, so the Delphi developers recommended using the .cube format instead. (The newer version of Delphi does not seem available for Mac at the moment.) Is the ValueError to do with ChimeraX or is it something to do with the .cube files? Do you have any suggestions as to how to solve this? Thank you very much for all your help, Maria

3 3

Re: [chimerax-users] unsubscribe to ChimeraX-users Digest, Vol 43, Issue 15
by Hua tiger 14 Jul '20

14 Jul '20

On Tue, Jul 14, 2020 at 11:31 AM <chimerax-users-request(a)cgl.ucsf.edu> wrote: > Send ChimeraX-users mailing list submissions to > chimerax-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > or, via email, send a message with subject or body 'help' to > chimerax-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimerax-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of ChimeraX-users digest..." > > > Today's Topics: > > 1. Re: re-assignment of mousemode (Elaine Meng) > 2. Re: re-assignment of mousemode (piskacek(a)post.cz) > 3. Re: re-assignment of mousemode (Elaine Meng) > 4. Fwd: [Chimera-users] re-assignment of mousemode (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Jul 2020 13:45:33 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: "<piskacek(a)post.cz>" <piskacek(a)post.cz> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] re-assignment of mousemode > Message-ID: <3BB2DAA6-5B94-4965-B973-F72CFA5E2CFC(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Another way to set pivot (without changing mouse-button functions) is by: > > (1) selecting an atom (Ctrl-click on the atom in the graphics window) that > you want as the center of rotation > (2) using menu: Actions... Set Pivot > > Elaine > > > On Jul 13, 2020, at 1:00 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > Hi Martin, > > It is not clear what you mean by "no response." Do you have a mouse > with a right button, or can you use trackpad + Alt as the right button? If > you click any other icons in the Right Mouse tab of the Toolbar, can you > successfully assign any of those other functions to the right mouse button? > > > > Maybe it is a misunderstanding of how the icons work: > > If it is working correctly, nothing will happen when you click a RIght > Mouse icon, except that there will be a light green box around that icon. > Clicking the icon only reassigns the function of the right mouse button, > but does not perform any action at that time. However, if you reassign to > pivot by clicking the Right Mouse pivot icon, for example, then later > clicking with the right mouse button (if you have one) on an atom will make > that atom the pivot point. > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> > > > > If you do not have a right mouse button, you can use the "mousemode" > command (instead of icons) to assign the function to a different mouse > button. > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > >> On Jul 13, 2020, at 9:02 AM, <piskacek(a)post.cz> <piskacek(a)post.cz> > wrote: > >> > >> Dear Authors of ChimeraX, > >> > >> I load and start to use your very useful program ChimeraX on Windows 10 > >> (Alienware 17 x64, I7-4900MQ 2.8GHz, RAM 32GB, GeForce GTX 780M), > >> > >> I could do the same and more as in PyMol, but > >> I have trouble with re-assignment of mousemode in window "Right Mouse" > >> as result is no response for re-assignment into Pivot or Rotate model > >> > >> I tried ChimeraX versions 0,93, 1.0 and 1.1 (daily version) w/o > improvement > >> > >> Please, could you help me > >> Thank you very much for support > >> > > > > > > _______________________________________________ > > ChimeraX-users mailing list > > ChimeraX-users(a)cgl.ucsf.edu > > Manage subscription: > > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > > > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Jul 2020 23:48:44 +0200 (CEST) > From: <piskacek(a)post.cz> > To: "ChimeraX Users Help" <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] re-assignment of mousemode > Message-ID: <KC.3Mchj.NQenTdcZLM.1V3DQy(a)seznam.cz> > Content-Type: text/plain; charset="utf-8" > > exactly? all as you described all this is not working > > > > I assigned what my wright? mouse should execute,? > > but if I try to apply this function on amino acid from my protein it is > not > working > > > > Should I need to activate my mousemode somehow? > > I? suppose, that ChimeraX? is not working properly on windows in my case > I need some correction of some script to solve some hidden conflict in > windows > > thank you very much for you help > -- > Martin Piskacek > Laboratory of Cancer Biology and Genetics? > www.piskacek.org > Department of Pathological Physiology > Faculty of Medicine > Masaryk University Brno > Kamenice 5 > 625 00 Brno > Czech Republic > > > ---------- P?vodn? e-mail ---------- > Od: Elaine Meng <meng(a)cgl.ucsf.edu> > Komu: <piskacek(a)post.cz> <piskacek(a)post.cz> > Datum: 13. 7. 2020 22:45:47 > P?edm?t: Re: [chimerax-users] re-assignment of mousemode > "Another way to set pivot (without changing mouse-button functions) is by: > > (1) selecting an atom (Ctrl-click on the atom in the graphics window) that > you want as the center of rotation > (2) using menu: Actions... Set Pivot > > Elaine > > > On Jul 13, 2020, at 1:00 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > Hi Martin, > > It is not clear what you mean by "no response." Do you have a mouse with > a > right button, or can you use trackpad + Alt as the right button? If you > click any other icons in the Right Mouse tab of the Toolbar, can you > successfully assign any of those other functions to the right mouse > button? > > > > Maybe it is a misunderstanding of how the icons work: > > If it is working correctly, nothing will happen when you click a RIght > Mouse icon, except that there will be a light green box around that icon. > Clicking the icon only reassigns the function of the right mouse button, > but > does not perform any action at that time. However, if you reassign to > pivot > by clicking the Right Mouse pivot icon, for example, then later clicking > with the right mouse button (if you have one) on an atom will make that > atom > the pivot point. > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> > > > > If you do not have a right mouse button, you can use the "mousemode" > command (instead of icons) to assign the function to a different mouse > button. > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > >> On Jul 13, 2020, at 9:02 AM, <piskacek(a)post.cz> <piskacek(a)post.cz> > wrote: > > >> > >> Dear Authors of ChimeraX, > >> > >> I load and start to use your very useful program ChimeraX on Windows 10 > >> (Alienware 17 x64, I7-4900MQ 2.8GHz, RAM 32GB, GeForce GTX 780M), > >> > >> I could do the same and more as in PyMol, but > >> I have trouble with re-assignment of mousemode in window "Right Mouse" > >> as result is no response for re-assignment into Pivot or Rotate model > >> > >> I tried ChimeraX versions 0,93, 1.0 and 1.1 (daily version) w/o > improvement > >> > >> Please, could you help me > >> Thank you very much for support > >> > > > > > > _______________________________________________ > > ChimeraX-users mailing list > > ChimeraX-users(a)cgl.ucsf.edu > > Manage subscription: > > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > > " >

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Fwd: [Chimera-users] re-assignment of mousemode
by Elaine Meng 14 Jul '20

14 Jul '20

sending to chimerax-users instead of chimera-users (I'd accidentally set the "reply-to" to the wrong list, sorry -- Elaine ) > Begin forwarded message: > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] [chimerax-users] re-assignment of mousemode > Date: July 14, 2020 at 8:25:20 AM PDT > To: "<piskacek(a)post.cz>" <piskacek(a)post.cz> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Reply-To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > > Hi Martin, > The "Pivot" function sets the center of rotation for the whole view, for when you rotate everything with the mouse. It does not rotate the bond. If you want to rotate the bond, instead use the "Bond rotation" mouse mode, the icon much further right on the same toolbar as shown in your image. > > The Right Mouse icons and what they mean are listed here: > <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On Jul 14, 2020, at 5:16 AM, <piskacek(a)post.cz> <piskacek(a)post.cz> wrote: >> >> Dear Elaine, >> thank you very much for your assistance, but >> I do everything correctly, but it just did not work = see figure >> I would like to rotate tryptofan in my figure, so as first I need to set pivot on the C-atom (designated here as CB) and than rotate with right mouse the tryptofan >> >> <Mail Attachment.png> > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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re-assignment of mousemode
by piskacek＠post.cz 13 Jul '20

13 Jul '20

Dear Authors of ChimeraX, I load and start to use your very useful program ChimeraX on Windows 10 (Alienware 17 x64, I7-4900MQ 2.8GHz, RAM 32GB, GeForce GTX 780M), I could do the same and more as in PyMol, but I have trouble with re-assignment of mousemode in window "Right Mouse" as result is no response for re-assignment into Pivot or Rotate model I tried ChimeraX versions 0,93, 1.0 and 1.1 (daily version) w/o improvement Please, could you help me Thank you very much for support -- Martin Piskacek Laboratory of Cancer Biology and Genetics www.piskacek.org Department of Pathological Physiology Faculty of Medicine Masaryk University Brno Kamenice 5 625 00 Brno Czech Republic

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ChimeraZ: show surface under another surface
by Anastasiya Oguienko 13 Jul '20

13 Jul '20

Dear ChimeraX developers, Hello! Thanks for this amazing tool, I enjoy every second of using it! I have a question about surface imaging: I have several subunits in the protein, and I would like to show surfaces of particular regions of different subunits. However, when one surface is above another, the lower one is not displayed no matter what the transparency value is. Is there a way to display both of the overlapping surfaces? Thanks in advance! -- With Best Regards, Anastasiya Oguienko

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Which color/palette was used
by Maria Maldonado 10 Jul '20

10 Jul '20

Hello, I was wondering if there’s a command that reports the color/palette of a chain/model. I saved a session with the palette I wanted, but didn’t make a note of what the palette was, and I would now like to use the same palette on a different session. Thank you for your help! Maria

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[chimeraX-users] to display cylinder and helical ribbon of one chain
by Yingyi Zhang 10 Jul '20

10 Jul '20

Dear ChimeraX Team, I have one model (pdb format), which contains multiple chains. Each chain (chain A for instance) consists of several helices. Is it possible to display ChainA in this manner - first two helices as cylinders but the others as ribbons? I tried to specify the residues, but it always changed the entire presence of the model, including the un-selected ones. Could you help me with this? I am still not very familiar with chimeraX. Thank you very much. Best regards, Yingyi

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Subscript in 2Dlabels
by Derek Harris 08 Jul '20

08 Jul '20

Is there a way, or code, to do sub/superscripts in a 2Dlabel? Derek Harris Postdoctoral Fellow Seefeldt Lab Department of Chemistry and Biochemistry Utah State University

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Re: [chimerax-users] label_seq_id in mmcif files for Chimera
by Greg Couch 08 Jul '20

08 Jul '20

On 7/7/2020 3:50 PM, Marcin Wojdyr wrote: > On Tue, 7 Jul 2020 at 22:38, Greg Couch <gregc(a)cgl.ucsf.edu> wrote: >> As you know, the entity_poly_seq table says which polymeric residues are >> adjacent to each other (entity_poly_seq.num values are the >> atom_site.label_seq_id values). > Yes, it's an enhanced equivalent of the SEQRES record in the PDB > format. Files from the wwPDB always have it, but files from other > sources will often miss it. I think currently almost all the mmCIF > files in circulation originate from the wwPDB. But this is slowly > changing and people are starting to use mmCIF as a working format. The sequence information is extremely useful for eliminating ambiguities in the atom_site data. And it is frequently known by the user, even when it is missing from the mmCIF file. >> Without that information, ChimeraX >> still needs the atom_site.label_seq_id to imply the polymeric ordering. > Ok. It would be useful, though, if ChimeraX could infer the ordering > and connectivity in the same way as it does for PDB files. > > Thanks, > Marcin Adding a atom_site.label_seq_id isn't different from supplying a residue number in PDB file. When there are adjacent residues of the same type, does the PDB reader see a duplicate atom and generate a new residue? merge the residues? generate an error? I haven't tested the PDB reader, but a residue number helps it too. Learning to use mmCIF effectively will take time. Programmers should use the PDB's mmCIF Dictionary Suite to validate the mmCIF their programs output -- it won't validate completely (because it's for mmCIF files served by the PDB), but it will show where the mmCIF output can be improved. For more information about ChimeraX reading mmCIF, see https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/mmcif/src/mmcif_guide…. ChimeraX's mmCIF reader tries really hard to show you the data exactly as it is specified. So if there's badly specified data, you'll be able to see it. Over time, we will improve ChimeraX's ability to handle underspecified data as developers start generating mmCIF files. But we don't plan to modify the mmCIF reader if we can help it. Adding code, to infer information that should be explicitly given in the mmCIF file, slows down the mmCIF reader for everyone. This is especially true for large structures with over a million atoms. -- Greg

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Re: [chimerax-users] [Chimera-users] Chimera X - Windows 7 home premium
by Greg Couch 08 Jul '20

08 Jul '20

(This is a ChimeraX question, so sending the reply to the chimerax-users mailing too.) Looking at the image, the three gray boxes are icons for previously opened data files. To get an interactive 3D image, you would need to open an appropriate data file. If you type in the command "open 3rec" and press Enter/Return afterwards to open PDB model 3rec, does an interactive 3D image show up? If you can't get an interactive 3D image, then you probably need a newer graphics driver. I'd recommend going to the Lenovo support web site and installing a newer graphics driver. If the driver from Lenovo doesn't fix the problem, then you'll need to get one directly from Intel at https://downloadcenter.intel.com/. From the DxDiag.txt output, you have a 2nd generation i7 with HD Graphics 3000 driver version 8.15.10.2656. Lenovo has version 8.15.10.2274 from 6/9/2011 for your computer. On the Intel site, I see that version 15.28.24.4229 from 6/5/2015 is available. And you should know that we don't test ChimeraX on Windows 7, so technically you are on an unsupported platform. That said, we are unaware of anything that would prevent ChimeraX from running on Windows 7. However, with the age of your laptop, you should consider switching from Windows to Ubuntu (Linux). Intel is still supporting the Linux graphics driver for older systems. HTH, Greg On 7/8/2020 7:29 AM, MONICA MESA CADAVID wrote: > I would like to use the new Chimera X. > I installed and open the program easily. > But the images did not appear. > I attach the information of my computer because I would like to know > if I can fix the problem. > Thank you > * > * > image.png > *Monica Mesa Cadavid* > Profesor Titular > Instituto de Quimica > Facultad de Ciencias Exactas y Naturales > monica.mesa(a)udea.edu.co <http://udea.edu.co/> > Grupo Ciencia de los Materiales > Sede de Investigacion Universitaria, SIU -Torre 1, laboratorio 310 > Cra 53 # 61 - 30 > Tel. 574 - 219 6546 > > http://www.udea.edu.co/ <http://www.udea.edu.co/> > > > > *Universidad de Antioquia* > www.udea.edu.co <http://www.udea.edu.co/> > Sede Principal: Cll 67 # 53 - 108 > Medellín, Colombia > > "La información aquí contenida es para uso exclusivo de la persona o > entidad de destino. Está estrictamente prohibida su utilización, > copia, descarga, distribución, modificación y/o reproducción total o > parcial, sin el permiso expreso de Universidad de Antioquia, pues su > contenido puede ser de carácter confidencial y/o contener material > privilegiado. Si usted recibió esta información por error, por favor > contacte en forma inmediata a quien la envió y borre este material de > su computador. Universidad de Antioquia no es responsable por la > información contenida en esta comunicación, el directo responsable es > quien la firma o el autor de la misma." > > > > "La información aquí contenida es para uso exclusivo de la persona o > entidad de destino. Está estrictamente prohibida su utilización, > copia, descarga, distribución, modificación y/o reproducción total o > parcial, sin el permiso expreso de Universidad de Antioquia, pues su > contenido puede ser de carácter confidencial y/o contener material > privilegiado. Si usted recibió esta información por error, por favor > contacte en forma inmediata a quien la envió y borre este material de > su computador. Universidad de Antioquia no es responsable por la > información contenida en esta comunicación, el directo responsable es > quien la firma o el autor de la misma." > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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ChimeraX bug report submission
by Nicco 08 Jul '20

08 Jul '20

The following bug report has been submitted: Platform: Darwin-19.3.0-x86_64-i386-64bit ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Hi, I'm trying to record a movie and the movie generated stops before executing all final steps. It's like the last frames are not recorded even when I see a very high limit. I feel like movie encode starts processing before it is called. For example these commands below are not present in the movie but the movie encode is called afterwards. # Select last interaction area select /F:370,375 /E:270,309,314 show sel atoms hbonds sel select clear # Final show turn x 15 60 rock 130 turn -y 15 60 rock 130 I'm a bit puzzled of why this is happening and I don't really now how to fix it. I attach the .cxc file with the set of instructions that I use to create the movie. Please consider that my experience level is beginner so there could be something that I'm doing wrong. Thank you! Nicco Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "/Users/niar/Dropbox (CRG > ADV)/Nicco/projects/06_Chimera/src/movies/6NQ3_Suz12_AS_event.cxc" > open 6NQ3 6nq3 title: Crystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric Complex [more info...] Chain information for 6nq3 #1 --- Chain | Description A E | Histone-binding protein RBBP4 B F | Polycomb protein SUZ12 C G | PHD finger protein 19 D H | Protein Jumonji Non-standard residues in 6nq3 #1 --- ZN — zinc ion 6nq3 mmCIF Assemblies --- 1| software_defined_assembly 2| software_defined_assembly > select all 11928 atoms, 12213 bonds, 30 pseudobonds, 3 models selected > show sel cartoons > style sel stick Changed 11928 atom styles > hide sel atoms > select /A,B,C,G,D,H 6565 atoms, 6720 bonds, 15 pseudobonds, 3 models selected > hide sel cartoons > select /E 3045 atoms, 3128 bonds, 2 pseudobonds, 2 models selected > color (#!1 & sel) purple > select /F 2318 atoms, 2365 bonds, 13 pseudobonds, 3 models selected > color (#!1 & sel) cyan > select clear > set bgColor white > lighting soft > graphics silhouettes true > view > view name start > movie record supersample 1 size 720,720 limit 5000 directory > /Users/niar/Desktop/tmp_chimera pattern Frame_n* > turn z -70 > turn x 24 > turn y -40 > view name hole > wait 5 > select sequence > EEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLP 1138 atoms, 1174 bonds, 1 model selected > color sel orange > select clear > wait 10 > select sequence NHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYT 540 atoms, 552 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence GHQKEGYGLSWNPNLSGHLLSASDDHTICLWD 500 atoms, 516 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence GHTAVVEDVSWHLLHESLFGSVADDQKLMIWD 512 atoms, 526 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence AHTAEVNCLSFNPYSEFILATGSADKTVALWD 488 atoms, 500 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence SHKDEIFQVQWSPHNETILASSGTDRRLNVWD 532 atoms, 546 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence GHTAKISDFSWNPNEPWVICSVSEDNIMQVWQ 522 atoms, 540 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence RKTFKVDDMLSKVEKMKGEQESH 299 atoms, 299 bonds, 1 model selected > color sel red > select clear > wait 10 > turn x 20 120 rock 120 > wait > turn y 35 150 rock 150 > wait > turn y 4 90 > wait > turn y 1 50 > wait > turn x 1 35 > wait > zoom 1.5 80 > wait > move x 0.75 15 > move y -0.75 15 > wait > view name side > select /E:9-28 /E:32-39 239 atoms, 242 bonds, 1 model selected > show sel atoms > hbonds sel 51 hydrogen bonds found > select clear > wait 20 > turn x 15 60 rock 60 > wait > turn y 15 60 rock 60 > wait > ~hbonds > select /E:9-28 /E:32-39 239 atoms, 242 bonds, 1 model selected > hide sel atoms > select clear > wait 5 > move y 0.75 15 > move x -0.75 15 > wait > zoom 0.5 80 > wait > turn -x 1 35 > wait > turn -y 1 50 > wait > view hole > move x 0.75 25 > move y -0.5 25 > wait 25 > turn x 0.5 25 > zoom 3 80 > wait 80 > turn x 0.75 25 > move y 0.5 25 > wait 25 > view name zoom1 > select /F:129 /E:409 /E:346 31 atoms, 29 bonds, 1 model selected > show sel atoms > color (#!1 & sel) byelement > hbonds sel 12 hydrogen bonds found > select clear > wait 15 > turn -y 15 120 rock 120 > wait > turn x 15 60 rock 130 > wait > wait 15 > view name zoom2 > turn y -1.5 25 > move x -0.5 25 > wait 25 > turn x -1 25 > turn z 1 25 > move x 0.4 25 > wait 25 > select /F:135 /E:285,304,330 34 atoms, 30 bonds, 1 model selected > show sel atoms > color (#!1 & sel) byelement > hbonds sel 11 hydrogen bonds found > select clear > turn y -10 120 rock 180 > wait > turn x 15 120 rock 120 > wait > wait 20 > view name zoom3 > zoom 0.5 50 > turn -y 1 150 > wait > move x 0.75 15 > wait > turn x 1 20 > wait > zoom 1.5 50 > select /F:370,375 /E:270,309,314 42 atoms, 37 bonds, 1 model selected > show sel atoms > hbonds sel 8 hydrogen bonds found > select clear > turn x 15 60 rock 130 > turn -y 15 60 rock 130 > movie status \-----Movie status------------------------------ Recording 1785 frames (in 'PPM' format) saved to directory '/Users/niar/Desktop/tmp_chimera' using pattern 'Frame_n*' . Est. movie length is 74.375s. \------------------------------------------------ > movie encode /Users/niar/Desktop/Suz12_test1.mp4 format h264 quality low > wait true verbose false Movie saved to /Users/niar/Desktop/Suz12_test1.mp4 executed 6NQ3_Suz12_AS_event.cxc OpenGL version: 4.1 INTEL-14.4.23 OpenGL renderer: Intel(R) Iris(TM) Graphics 6100 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro12,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2,7 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 3 MB Hyper-Threading Technology: Enabled Memory: 8 GB Boot ROM Version: 189.0.0.0.0 SMC Version (system): 2.28f7 Software: System Software Overview: System Version: macOS 10.15.3 (19D76) Kernel Version: Darwin 19.3.0 Time since boot: 1 day 20:31 Graphics/Displays: Intel Iris Graphics 6100: Chipset Model: Intel Iris Graphics 6100 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x162b Revision ID: 0x0009 Metal: Supported, feature set macOS GPUFamily1 v4 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal HP LP2065: Resolution: 1600 x 1200 (UXGA - Ultra eXtended Graphics Array) UI Looks like: 1600 x 1200 @ 60 Hz Framebuffer Depth: 24-Bit Color (ARGB8888) Display Serial Number: CNG70302V3 Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 File attachment: 6NQ3_Suz12_AS_event.cxc

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Re: [chimerax-users] [Chimera-users] Difference in alignment of cofactor between Chimera and ChimeraX
by Elaine Meng 07 Jul '20

07 Jul '20

Hello Derek, You're welcome! Thought I should also mention that in matchmaker you can specify more than one pair of chains, i.e. use multiple pairs of chains for the fit. Which way is better depends on what you are trying to achieve: overall superposition of whole complex, or best fit of a single pair of chains. This multichain fit can be done in either Chimera or ChimeraX with a matchmaker command option. I'll use ChimeraX commands to illustrate: open 3u7q open 5n6y hide ribbon The ChimeraX log shows that 3u7q has four chains, two alpha (A,C) and two beta (B,D) whereas 5n6y has 6 chains, two alpha (A,D), two beta (B,E) and two delta (C,F). So perhaps you want to use all of the alpha and beta chains from the structures for the fit instead of only A with A. Now the trick is to figure out which alpha goes with which alpha and which beta with which beta. I might be lazy and first just try ABCD in 3u7q as pairing with ABDE in 5n6y and see if that looks right. I might also use coloring by polymer (figures out a color based on chain sequence) to make it clearer what's what. color bypolymer mm #2/A,B,D,E to #1/A,B,C,D pair ss <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> .... which actually looks right. The alphas and betas are colored the same within a given PDB structure but different between the structures, probably because of small sequence differences (something like one structure has a couple more residues on one end or the other; I didn't investigate, but it's expected). The Log reports: RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) ...now to check the placement of cofactors: show ligand ~ribbon You can see a more symmetrical fit, with similar displacements on both sides. I hope this helps, Elaine > On Jul 7, 2020, at 9:39 AM, Derek Harris <derek.harris(a)aggiemail.usu.edu> wrote: > > Hello Elaine, > > Thank you very much for the rapid response. Following your commands, and seeing all the ligands, I now see what's happening. Just as you said; the proteins are each composed of two identical catalytic halves. In one half there is a nice alignment of the cofactors, but in the other half there is not. I was isolating, and only viewing, the chain where there isn't good alignment. > > Thanks again! > > Derek Harris > Postdoctoral Fellow > Seefeldt Lab > Department of Chemistry and Biochemistry > Utah State University > > > On Tue, Jul 7, 2020 at 9:35 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hello Derek, > It does not make sense for the cofactor alignment to be different if the protein alignment is the same, because the cofactors are just moved rigidly along with their proteins. Also the results should be identical between Chimera and ChimeraX, assuming you are using the same options. > > I get exactly the same alignment between these two proteins in the Chimera vs. ChimeraX. > > Chimera commands (including display ligand only): > open 3u7q > open 5n6y > mm #0 #1 > ~ribbon > show ligand > > ChimeraX commands: > open 3u7q > open 5n6y > mm #2 to #1 > ~ribbon > hide > show ligand > > In both programs, I get the same RMSD message to the Log: > > RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998) > > In both programs, matchmaker ends up choosing to align chain A to chain A. Thus the cofactors in chains A are better superimposed than the ones in the other chains. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Jul 6, 2020, at 6:47 PM, Derek Harris <derek.harris(a)aggiemail.usu.edu> wrote: > > > > Hello, > > > > I am trying to reproduce an alignment I had previously done in Chimera in ChimeraX with matchmaker command. > > > > The protein alignment between the two programs is the same, but in ChimeraX the active-site cofactor of the matchstruct isn't aligning appropriately to the refstruct cofactor and is unreasonably placed in relation to even its own protein. In Chimera the two cofactors align nicely. > > > > The two structures I am trying to align are 3U7Q and 5N6Y. > > > > Thanks in advance for any assistance you can offer! > > > > Derek Harris > > Postdoctoral Fellow > > Seefeldt Lab > > Department of Chemistry and Biochemistry > > Utah State University > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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how to turn molecule centering a specific atom in ChimeraX
by Shin Inchul 07 Jul '20

07 Jul '20

Hi, I was trying to turn molecule around specific atom. Since I am a beginner of ChimeraX, I would like to have some working examples in the command line. Without it, I have difficulties in applying the usage as appeared in the user guide. In PyMOL, mouse middle button click on a atom sets the centering on the atom then use rotate command. I appreciate all the supports provided. Thank you. Inchul

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Re: [chimerax-users] session file sizes
by Tom Goddard 07 Jul '20

07 Jul '20

To close molecular surfaces surface close #1 or just surf close If instead you do ~surface that hides the surface. I discourage use of these obscure "~" commands that Chimera used. Use "surface hide #1" or "surface close #1". If you just hide the surfaces they are still in the session file. You can also see the surface models in Model Panel by clicking the little triangle and the left of the model name to show submodel of your molecule. And you can choose those surface models and close them. Tom > On Jul 7, 2020, at 2:48 PM, Melissa Jurica <mjurica(a)ucsc.edu> wrote: > > That was my first guess, so I turned off the surface view. However, no change in file size. I don’t see how to delete the surface that I calculated- still trying to get the hang of ChimeraX after switching from Chimera. > > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > Melissa S. Jurica, Ph.D. > Professor, Molecular, Cell & Developmental Biology > Center for Molecular Biology of RNA > University of California, Santa Cruz > 1156 High Street > Santa Cruz, CA 95064 > > Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs > Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 > http://www.mcd.ucsc.edu/faculty/jurica.html <http://www.mcd.ucsc.edu/faculty/jurica.html> > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > >> On Jul 7, 2020, at 2:41 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Melissa, >> >> Molecular surfaces make session files very large because they save all the surface triangles. Did you have a molecular surface in that large session? I have considered not saving the molecular surfaces and just recomputing them although that will make restoring the session slower as it tries to recompute the surface. >> >> Tom >> >> >>> On Jul 7, 2020, at 2:28 PM, Melissa Jurica <mjurica(a)ucsc.edu <mailto:mjurica@ucsc.edu>> wrote: >>> >>> What deterimines the file size of saved ChimeraX sessions (.csx files)? I saved a session of one structure (6Y5q) at 4 MB, and another structure (6y50) at 2.6 MB. However, when I saved a session with both structures open, it was a whopping 120.6 MB. Is there a way to reduce that file size? >>> >>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>> Melissa S. Jurica, Ph.D. >>> Professor, Molecular, Cell & Developmental Biology >>> Center for Molecular Biology of RNA >>> University of California, Santa Cruz >>> 1156 High Street >>> Santa Cruz, CA 95064 >>> >>> Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs >>> Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 >>> http://www.mcd.ucsc.edu/faculty/jurica.html <http://www.mcd.ucsc.edu/faculty/jurica.html> >>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >> >

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session file sizes
by Melissa Jurica 07 Jul '20

07 Jul '20

What deterimines the file size of saved ChimeraX sessions (.csx files)? I saved a session of one structure (6Y5q) at 4 MB, and another structure (6y50) at 2.6 MB. However, when I saved a session with both structures open, it was a whopping 120.6 MB. Is there a way to reduce that file size? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Melissa S. Jurica, Ph.D. Professor, Molecular, Cell & Developmental Biology Center for Molecular Biology of RNA University of California, Santa Cruz 1156 High Street Santa Cruz, CA 95064 Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 http://www.mcd.ucsc.edu/faculty/jurica.html <http://www.mcd.ucsc.edu/faculty/jurica.html> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

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label_seq_id in mmcif files for Chimera
by Marcin Wojdyr 07 Jul '20

07 Jul '20

Hi, I'd like to generate mmCIF files (using my own software) that can be read by Chimera. The problem is that sometimes I don't know the full sequence (SEQRES), so I don't know values for _atom_site.label_seq_id. If I skip label_seq_id entirely, the file doesn't load. ChimeraX gives warning: "Skipping atom_site category: Missing column 'label_seq_id'". If I set all label_seq_id values to null ('.') I get warning: "Unable to infer polymer connectivity due to unspecified label_seq_id for residue "ARG" near line 125" and all residues are disconnected. How should the mmCIF look like so that Chimera infers the connectivity in the same way as it does for PDB files? Cheers, Marcin

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Re: [chimerax-users] [ChimeraX] #3464: partial surface mesh
by Elaine Meng 07 Jul '20

07 Jul '20

Hi Rory, There is no "hydrophobic surface" ... maybe you mean the molecular surface shown as solid (not dot or mesh)? Chimera's presets include "hydrophobicity surface" which is perhaps misleading, simply means the molecular surface colored by hydrophobicity. What exactly are you trying to do? Show protein as mesh surface and ligand as solid surface? You can definitely do it (or any combination of mesh surface on some atoms, solid on some other atoms) by opening multiple copies of the structure, as we said in previous messages. Then in the solid-surface copy, only show the parts of the surface you want as solid. In the mesh-surface copy, show the parts you want as mesh. For example, here is an example that shows H-ras as mesh surface with its ligand GCP as solid surface (image attached below), commands: open 121p open 121p surf #1 & protein surf #2:gcp surf style #1 mesh transp #1 50 surfaces color #2 gold surfaces hide solvent This can all be done with the menu as well, but it would take a lot more typing to enter that whole procedure. I Cc'd chimerax-users(a)cgl.ucsf.edu which is the recommended address for asking ChimeraX questions (for future reference). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 6, 2020, at 10:30 AM, Gordon, Rory <rory.gordon.19(a)ucl.ac.uk> wrote: > > Hi Guys, > > Further to previous email, just tried fiddling with the transparency settings. > > I can get the protein structure to change through the transparency gradient for hydrophobic surface. > > However, for the substrate/ligands there seems to be binary system where you can either have full transparency or none at all. > > The hydrophobic surface can be coloured both for the protein and substrate/ligand. > > Cheers, > > Rory > From: Gordon, Rory <rory.gordon.19(a)ucl.ac.uk> > Sent: 06 July 2020 18:26 > To: Tom Goddard <goddard(a)sonic.net>; Elaine Meng <meng(a)cgl.ucsf.edu> > Cc: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [ChimeraX] #3464: partial surface mesh > > Hi Tom, Elaine and Eric > > I tried to establish the mesh surface with the whole protein structure selected through the GUI. I can only get the hydrophobic surface which I can colour with B-factor. > > The options of Mesh, Dot or Solid don't seem to change anything. > > Not sure how to get round this, so any help would be appreciated. > > Cheers, > > Rory > > > From: Tom Goddard <goddard(a)sonic.net> > Sent: 02 July 2020 18:24 > To: Elaine Meng <meng(a)cgl.ucsf.edu> > Cc: Gordon, Rory <rory.gordon.19(a)ucl.ac.uk>; Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [ChimeraX] #3464: partial surface mesh > > Another trick that makes these meshes look nicer is to make them about 50-80% transparent (command "transp #2 70"). It gives the mesh an airy look. > > Tom > > >> On Jul 2, 2020, at 10:17 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi Rory, >> Here is an example image where I opened the same structure twice. I showed one copy with mesh surface and the second one with solid surface, and then simply hid parts of the solid surface. This is the way that Tom mentioned. >> Elaine >> >> <example.png> >> >> >>> On Jul 2, 2020, at 3:29 AM, ChimeraX <ChimeraX-bugs-admin(a)cgl.ucsf.edu> wrote: >>> >>> #3464: partial surface mesh >>> ---------------------------------------+---------------------------- >>> Reporter: rory.gordon.19@… | Owner: Eric Pettersen >>> Type: defect | Status: closed >>> Priority: normal | Milestone: >>> Component: Surface | Version: >>> Resolution: fixed | Keywords: >>> Blocked By: | Blocking: >>> Notify when closed: | Platform: all >>> Project: ChimeraX | >>> ---------------------------------------+---------------------------- >>> >>> Comment (by rory.gordon.19@…): >>> >>> {{{ >>> Hi Eric, >>> >>> Thanks for your email. >>> >>> I had actually seen a graphic in a publication which gave me that idea. >>> >>> Thanks anyway for the pointers. >>> >>> Cheers, >>> >>> Rory >>> ________________________________ >>> From: ChimeraX <ChimeraX-bugs-admin(a)cgl.ucsf.edu> >>> Sent: 01 July 2020 18:23 >>> Cc: goddard(a)cgl.ucsf.edu <goddard(a)cgl.ucsf.edu>; meng(a)cgl.ucsf.edu >>> <meng(a)cgl.ucsf.edu>; pett(a)cgl.ucsf.edu <pett(a)cgl.ucsf.edu>; Gordon, Rory >>> <rory.gordon.19(a)ucl.ac.uk> >>> Subject: Re: [ChimeraX] #3464: partial surface mesh (was: ChimeraX bug >>> report submission) >>> >>> #3464: partial surface mesh >>> ---------------------------------------+---------------------------- >>> Reporter: rory.gordon.19@… | Owner: Eric Pettersen >>> Type: defect | Status: accepted >>> Priority: normal | Milestone: >>> Component: Unassigned | Version: >>> Resolution: | Keywords: >>> Blocked By: | Blocking: >>> Notify when closed: | Platform: all >>> Project: ChimeraX | >>> ---------------------------------------+---------------------------- >>> Changes (by Eric Pettersen): >>> >>> * status: new => accepted >>> * cc: Tom Goddard, Elaine Meng (added) >>> * project: => ChimeraX >>> * platform: => all >>> * owner: (none) => Eric Pettersen >>> >>> >>> Comment: >>> >>> Hi Rory, >>> I don't believe you can change just part of a surface into mesh, >>> it's all or nothing. You can make that part of the surface partially >>> transparent instead with Actions→Surface→Transparency. >>> >>> --Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>> ----- >>> Tom, should the command "surface style (#!4 & sel) mesh" actually do >>> nothing (with part of the surface selected)? That seems surprising. >>> Seems like it should change the whole surface into mesh. Is that a bug >>> or >>> am I misunderstanding something? >>> >>> --Eric >>> >>> -- >>> Ticket URL: >>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl…> >>> ChimeraX >>> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u…> >>> ChimeraX Issue Tracker >>> }}} >>> >>> -- >>> Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3464#comment:7> >>> ChimeraX <http://www.rbvi.ucsf.edu/chimerax/> >>> ChimeraX Issue Tracker

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artificial lines or seems on surface using soft lighting
by Steve Chou 06 Jul '20

06 Jul '20

Hi ChimeraX folks, When I used soft lighting, I saw lines/seams on the molecular surface (see the attached image). To reproduce this: ---------------------- load xxxx.pdb surface color violet lighting soft ---------------------- How to remove these artificial lines/seams? These lines also show up in the cutting plane in a section view. Many thanks in advance! Steve -- Steve Chou

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Can I only clip some models, but not all of them?
by Steve Chou 05 Jul '20

05 Jul '20

Hi ChimeraX developers and users, When a ligand is embedded in the protein, can I only clip the surface of the protein, but not the ligand (sticks)? Many thanks, Steve -- Steve Chou

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How to obtain size measures
by Andrea Dallapè 04 Jul '20

04 Jul '20

Dear UCSF Chimera and ChimeraX developers, I would like to ask you if there's a method to obtain the size measures of a protein in order to compare with the heights and lengths obtained by AFM. Could you please suggest me how could I obtain such measurements? Thank you in advance for your help and support, Andrea

2 2

color offset and surface type for mapping Electrostatic Potential
by Steve Chou 02 Jul '20

02 Jul '20

Hello everyone, I tried to map Electrostatic Potential (ESP) onto the molecular surface in ChimeraX v1.0 and PyMOL v2.1, but I found that the results were very different in these two programs. Therefore, I wrote to Elaine Meng and Tom Goddard for help. For your reference, I repost the ideals of our emails below. I first calculated the ESP with DelPhi v5.1 (a relatively old version) to get the .phi file (ESP). PyMOL commands for displaying ESP on the molecular surface are as follows: ------------------------------------------------ load 1ubq.pdb bg_color white remove resn hoh remove hydrogens hide line select heavy, name c*+o*+s*+n* show surface load 1ubq.phi, e_map ramp_new e_lvl, e_map, [-7, 0, 7] set surface_color, e_lvl, 1ubq set light_count, 1 set ambient, 0.5 set reflect, 0.2 ------------------------------------------------ ChimeraX commands for displaying ESP on the molecular surface are as follows: ------------------------------------------------ open 1ubq.pdb open 1ubq.phi hide #2 set bg white surface #1 color electrostatic #1 map #2 palette -7,red:0,white:7,blue material dull lighting simple ------------------------------------------------ In PyMOL, the colors (red/blue) are mainly on the residue (E/D, K/R) tips, while in ChimeraX, the colors are spread. Besides, the surface shapes are also slightly different in these two programs. See the image (left and middle panels) for the different colors and shapes. The color difference is caused by the color offset. The shape difference is also explained below. I changed the color offset to 0. Now the color looks similar in these two programs (left and right panels). The color offset (1.4 A) in ChimeraX gives a better idea of the possible charge interactions with other molecules. ------------------------------------------------ color electrostatic #1 map #2 palette -7,red:0,white:7,blue offset 0.0 ------------------------------------------------ The summary of the explanations from Tom: ------------------------------------------------ One idea I have for why PyMol shows redder tips is because ChimeraX is showing the potential 1.4 Angstroms away from the surface since that is about how far away a binding molecule would be. PyMol may be showing the ESP values exactly on the surface. You can try using 0 offset instead of 1.4 with the "color electrostatic" command "offset" parameter. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#map ------------------------------------------------ The summary of the explanations from Elaine: ------------------------------------------------ As Tom mentioned, the rationale for the 1.4 A projection is that Chimera and ChimeraX show the solvent-excluded surface (SES), as opposed to the solvent-accessible surface (SAS). The SAS is approximately half a probe radius outward, and the SAS represents the closest possible approach of atomic centers of waters or ligands interacting with the protein, so the result is coloring by what values of the electrostatic potential (ESP) that such ligands would "see". The diagram in this page shows the relationships among SES, SAS, and probe. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> Possible reasons for difference in Pymol, if the ESP map itself is identical: (1) coloring by offset values or not. It has been my general understanding that when programs color the SES by ESP, the default approach is to color by the values one surface-probe radius outward. (2) shape/location of the surface. Is it an SES or SAS, or neither? Pymol surfaces often look more "melty" or smoothed to me than the SES in Chimera/ChimeraX. (3) the exact color-mapping, i.e. which colors at which values. Pymol ESP coloring often uses a duller-looking blue. ------------------------------------------------ All the best, Steve -- Steve Chou

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color key
by Roberto Marabini 02 Jul '20

02 Jul '20

hi, Is there a colorkey command in chimeraX (http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels…>)? If it does not exist, is there any alternative other than using chimera and photoshop? Thanks Roberto

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Is color command slower in ChimeraX than Chimera?
by Mungo Carstairs (Staff) 30 Jun '20

30 Jun '20

Hi, I'm testing driving ChimeraX (or Chimera) from Jalview, in particular colouring structures using the Jalview alignment residue colouring. Ideally this should perform well at scale for large numbers of structures and/or colours (for example a graduated colouring based on some property). I've noticed that ChimeraX appears to do this slower than Chimera. Is there a reason, or something I should do to make the command faster? Here's an example like for like comparison using the Chimera/X command line (also attached as a text file): Chimera 1.15 (build 42156) > open cifID:4zho cifID:5h92 cifID:1a70 cifID:4zhp > focus > color #977b64 #0:2.A,2.B;color #e46daf #0:3.A,3.B;color #7dc891 #0:4.A,4.B;color #768daf #0:5.A,5.B;color #bb1691 #0:6.A,6.B;color #1c5355 #0:7.A,7.B;color #5b1873 #0:8.A,8.B;color #d0af91 #0:9.A,9.B;color #6cb737 #0:10.A,10.B;color #8d7c55 #0:11.A,11.B;color #844173 #0:12.A,12.B;color #1f15a0 #0:13.A,13.B;color #a27f91 #0:14.A,14.B;color #19cb64 #0:15.A,15.B;color #484537 #0:16.A,16.B;color #61be37 #0:17.A,17.B;color #84a173 #0:18.A,18.B;color #c76691 #0:19.A,19.B;color #8f31a0 #0:20.A,20.B;color #9eb9af #0:21.A,21.B;color #531564 #0:22.A,22.B;color #707046 #0:23.A,23.B;color #9b80af #0:24.A,24.B;color #ca18a0 #0:25.A,25.B;color #377382 #0:26.A,26.B;color #26a137 #0:27.A,27.B;color #d3b1a0 #0:28.A,28.B;color #e267af #0:29.A,29.B;color #c023af #0:30.A,30.B;color #b18da0 #0:31.A,31.B;color #88bb55 #0:32.A,32.B;color #1fada0 #0:33.A,33.B;color #b22773 #0:34.A,34.B;color #ad19be #0:35.A,35.B;color #6483af #0:36.A,36.B;color #c9de91 #0:37.A,37.B;color #aab2be #0:38.A,38.B;color #59d164 #0:39.A,39.B;color #6d6037 #0:40.A,40.B;color #1cd937 #0:41.A,41.B;color #b5cb82 #0:42.A,42.B;color #e28191 #0:43.A,43.B;color #9537a0 #0:44.A,44.B;color #d6b0a0 #0:45.A,45.B;color #3bcf46 #0:46.A,46.B;color #2c6737 #0:47.A,47.B;color #e586af #0:48.A,48.B;color #e22daf #0:49.A,49.B;color #e29d91 #0:50.A,50.B;color #493582 #0:51.A,51.B;color #cacca0 #0:52.A,52.B;color #7f2855 #0:53.A,53.B;color #86dd91 #0:54.A,54.B;color #b55764 #0:55.A,55.B;color #4ac155 #0:56.A,56.B;color #614a37 #0:57.A,57.B;color #9e69af #0:58.A,58.B;color #5f8855 #0:59.A,59.B;color #958fa0 #0:60.A,60.B;color #9e45af #0:61.A,61.B;color #b9beaf #0:62.A,62.B;color #4add55 #0:63.A,63.B;color #5ba273 #0:64.A,64.B;color #bedf37 #0:65.A,65.B;color #359546 #0:66.A,66.B;color #262d37 #0:67.A,67.B;color #cf5bbe #0:68.A,68.B;color #505c46 #0:69.A,69.B;color #76db37 #0:70.A,70.B;color #3d37be #0:71.A,71.B;color #a28391 #0:72.A,72.B;color #b5cf64 #0:73.A,73.B;color #88b2a0 #0:74.A,74.B;color #bb4a91 #0:75.A,75.B;color #dc8755 #0:76.A,76.B;color #d579a0 #0:77.A,77.B;color #7c9846 #0:78.A,78.B;color #b57b82 #0:79.A,79.B;color #79cd46 #0:80.A,80.B;color #aa1abe #0:81.A,81.B;color #ab4873 #0:82.A,82.B;color #c6df91 #0:83.A,83.B;color #b3b3be #0:84.A,84.B;color #802d91 #0:85.A,85.B;color #d9c4af #0:86.A,86.B;color #c64d91 #0:87.A,87.B;color #857b46 #0:88.A,88.B;color #a26d91 #0:89.A,89.B;color #c62991 #0:90.A,90.B;color #adb1a0 #0:91.A,91.B;color #584991 #0:92.A,92.B;color #93b382 #0:93.A,93.B;color #48e137 #0:94.A,94.B;color #88c56f #1:1.C;color #7b5d60 #1:2.C;color #32d660 #1:3.C;color #339b7e #1:4.C;color #702460 #1:5.C;color #6725ba #1:6.C;color #dc536f #1:7.C;color #a3db7e #1:8.C;color #a8918d #1:9.C;color #d84eba #1:10.C;color #758b7e #1:11.C;color #88d751 #1:12.C;color #75ab7e #1:13.C;color #8e527e #1:14.C;color 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#768dcd #3:5.A;color #bb16af #3:6.A;color #1c5373 #3:7.A;color #3727a0 #3:8.A;color #d0afaf #3:9.A;color #6cb755 #3:10.A;color #8d7c73 #3:11.A;color #26d755 #3:12.A;color #1f15be #3:13.A;color #7e3464 #3:14.A;color #df35be #3:15.A;color #484555 #3:16.A;color #9764cd #3:17.A;color #84a191 #3:18.A;color #c766af #3:19.A;color #6f9a55 #3:20.A;color #9eb9cd #3:21.A;color #531582 #3:22.A;color #707064 #3:23.A;color #9b80cd #3:24.A;color #d0dbaf #3:25.A;color #3773a0 #3:26.A;color #26a155 #3:27.A;color #414855 #3:28.A;color #e267cd #3:29.A;color #c023cd #3:30.A;color #b18dbe #3:31.A;color #84d991 #3:32.A;color #1fadbe #3:33.A;color #bc63cd #3:34.A;color #ad19dc #3:35.A;color #6483cd #3:36.A;color #c9deaf #3:37.A;color #aab2dc #3:38.A;color #59d182 #3:39.A;color #6d6055 #3:40.A;color #1cd955 #3:41.A;color #b5cba0 #3:42.A;color #e281af #3:43.A;color #9537be #3:44.A;color #d6b0be #3:45.A;color #3bcf64 #3:46.A;color #2c6755 #3:47.A;color #e586cd #3:48.A;color #e22dcd #3:49.A;color #e29daf #3:50.A;color #4935a0 #3:51.A;color #caccbe #3:52.A;color #d573be #3:53.A;color #e229cd #3:54.A;color #b55782 #3:55.A;color #e449cd #3:56.A;color #614a55 #3:57.A;color #9e69cd #3:58.A;color #5f8873 #3:59.A;color #958fbe #3:60.A;color #9e45cd #3:61.A;color #975564 #3:62.A;color #1cdd73 #3:63.A;color #5ba291 #3:64.A;color #bedf55 #3:65.A;color #359564 #3:66.A;color #262d55 #3:67.A;color #711fa0 #3:68.A;color #505c64 #3:69.A;color #662773 #3:70.A;color #d319be #3:71.A;color #e2a1cd #3:72.A;color #b5cf82 #3:73.A;color #88b2be #3:74.A;color #bb4aaf #3:75.A;color #dc8773 #3:76.A;color #d579be #3:77.A;color #7c9864 #3:78.A;color #9d6c91 #3:79.A;color #79cd64 #3:80.A;color #aa1adc #3:81.A;color #ab4891 #3:82.A;color #1ca373 #3:83.A;color #8b4a73 #3:84.A;color #802daf #3:85.A;color #d9c4cd #3:86.A;color #c64daf #3:87.A;color #857b64 #3:88.A;color #a26daf #3:89.A;color #c629af #3:90.A;color #adb1be #3:91.A;color #5849af #3:92.A;color #93b3a0 #3:93.A;color #48e155 #3:94.A;color #93d3a0 #3:95.A;color #dc4d73 #3:96.A;color #d53fbe #3:97.A;color #6a4f55 #3:98.A On my Macbook these color commands take about 2 seconds. ChimeraX 1.0 (2020-06-04): > open pdb:4zho pdb:5h92 pdb:1a70 pdb:4zhp > view > color #1/A:2/B:2 #977b64;color #1/A:3/B:3 #e46daf;color #1/A:4/B:4 #7dc891;color #1/A:5/B:5 #768daf;color #1/A:6/B:6 #bb1691;color #1/A:7/B:7 #1c5355;color #1/A:8/B:8 #5b1873;color #1/A:9/B:9 #d0af91;color #1/A:10/B:10 #6cb737;color #1/A:11/B:11 #8d7c55;color #1/A:12/B:12 #844173;color #1/A:13/B:13 #1f15a0;color #1/A:14/B:14 #a27f91;color #1/A:15/B:15 #19cb64;color #1/A:16/B:16 #484537;color #1/A:17/B:17 #61be37;color #1/A:18/B:18 #84a173;color #1/A:19/B:19 #c76691;color #1/A:20/B:20 #8f31a0;color #1/A:21/B:21 #9eb9af;color #1/A:22/B:22 #531564;color #1/A:23/B:23 #707046;color #1/A:24/B:24 #9b80af;color #1/A:25/B:25 #ca18a0;color #1/A:26/B:26 #377382;color #1/A:27/B:27 #26a137;color #1/A:28/B:28 #d3b1a0;color #1/A:29/B:29 #e267af;color #1/A:30/B:30 #c023af;color #1/A:31/B:31 #b18da0;color #1/A:32/B:32 #88bb55;color #1/A:33/B:33 #1fada0;color #1/A:34/B:34 #b22773;color #1/A:35/B:35 #ad19be;color #1/A:36/B:36 #6483af;color #1/A:37/B:37 #c9de91;color #1/A:38/B:38 #aab2be;color #1/A:39/B:39 #59d164;color #1/A:40/B:40 #6d6037;color #1/A:41/B:41 #1cd937;color #1/A:42/B:42 #b5cb82;color #1/A:43/B:43 #e28191;color #1/A:44/B:44 #9537a0;color #1/A:45/B:45 #d6b0a0;color #1/A:46/B:46 #3bcf46;color #1/A:47/B:47 #2c6737;color #1/A:48/B:48 #e586af;color #1/A:49/B:49 #e22daf;color #1/A:50/B:50 #e29d91;color #1/A:51/B:51 #493582;color #1/A:52/B:52 #cacca0;color #1/A:53/B:53 #7f2855;color #1/A:54/B:54 #86dd91;color #1/A:55/B:55 #b55764;color #1/A:56/B:56 #4ac155;color #1/A:57/B:57 #614a37;color #1/A:58/B:58 #9e69af;color #1/A:59/B:59 #5f8855;color #1/A:60/B:60 #958fa0;color #1/A:61/B:61 #9e45af;color #1/A:62/B:62 #b9beaf;color #1/A:63/B:63 #4add55;color #1/A:64/B:64 #5ba273;color #1/A:65/B:65 #bedf37;color #1/A:66/B:66 #359546;color #1/A:67/B:67 #262d37;color #1/A:68/B:68 #cf5bbe;color #1/A:69/B:69 #505c46;color #1/A:70/B:70 #76db37;color #1/A:71/B:71 #3d37be;color #1/A:72/B:72 #a28391;color #1/A:73/B:73 #b5cf64;color #1/A:74/B:74 #88b2a0;color #1/A:75/B:75 #bb4a91;color #1/A:76/B:76 #dc8755;color #1/A:77/B:77 #d579a0;color #1/A:78/B:78 #7c9846;color #1/A:79/B:79 #b57b82;color #1/A:80/B:80 #79cd46;color #1/A:81/B:81 #aa1abe;color #1/A:82/B:82 #ab4873;color #1/A:83/B:83 #c6df91;color #1/A:84/B:84 #b3b3be;color #1/A:85/B:85 #802d91;color #1/A:86/B:86 #d9c4af;color #1/A:87/B:87 #c64d91;color #1/A:88/B:88 #857b46;color #1/A:89/B:89 #a26d91;color #1/A:90/B:90 #c62991;color #1/A:91/B:91 #adb1a0;color #1/A:92/B:92 #584991;color #1/A:93/B:93 #93b382;color #1/A:94/B:94 #48e137;color #2/C:1 #88c56f;color #2/C:2 #7b5d60;color #2/C:3 #32d660;color #2/C:4 #339b7e;color #2/C:5 #702460;color #2/C:6 #6725ba;color #2/C:7 #dc536f;color #2/C:8 #a3db7e;color #2/C:9 #a8918d;color #2/C:10 #d84eba;color #2/C:11 #758b7e;color #2/C:12 #88d751;color #2/C:13 #75ab7e;color #2/C:14 #8e527e;color #2/C:15 #cf53d8;color #2/C:16 #dc636f;color #2/C:17 #7d288d;color #2/C:18 #707460;color #2/C:19 #6fde51;color #2/C:20 #35a960;color #2/C:21 #627d8d;color #2/C:22 #bb42ab;color #2/C:23 #327060;color #2/C:24 #a3357e;color #2/C:25 #28bd8d;color #2/C:26 #8f91ba;color #2/C:27 #c856d8;color #2/C:28 #795760;color #2/C:29 #c067c9;color #2/C:30 #669b6f;color #2/C:31 #adabd8;color #2/C:32 #889d51;color #2/C:33 #c18f9c;color #2/C:34 #26bd51;color #2/C:35 #55cdba;color #2/C:36 #7e1a60;color #2/C:37 #238451;color #2/C:38 #68678d;color #2/C:39 #6da451;color #2/C:40 #a315d8;color #2/C:41 #88256f;color #2/C:42 #1f17ba;color #2/C:43 #4a456f;color #2/C:44 #6da051;color #2/C:45 #a4bfc9;color #2/C:46 #9557ba;color #2/C:47 #d6d0ba;color #2/C:48 #791d60;color #2/C:49 #e2e1ab;color #2/C:50 #1c616f;color #2/C:51 #7fda6f;color #2/C:52 #8e907e;color #2/C:53 #77559c;color #2/C:54 #c4bf8d;color #2/C:55 #77759c;color #2/C:56 #1658d8;color #2/C:57 #add1d8;color #2/C:58 #aa5aba;color #2/C:59 #95d3ba;color #2/C:60 #adadd8;color #2/C:61 #aa36ba;color #2/C:62 #95afba;color #2/C:63 #aa74d8;color #2/C:64 #731bd8;color #2/C:65 #442b6f;color #2/C:66 #8f1dba;color #2/C:67 #882d51;color #2/C:68 #9b2eab;color #2/C:69 #764d51;color #2/C:70 #6adb51;color #2/C:71 #359160;color #2/C:72 #e283ab;color #2/C:73 #ddb160;color #2/C:74 #cab2ba;color #2/C:75 #5559ba;color #2/C:76 #8a876f;color #2/C:77 #c76aab;color #2/C:78 #62a76f;color #2/C:79 #793f60;color #2/C:80 #23be51;color #2/C:81 #bab09c;color #2/C:82 #99397e;color #2/C:83 #a42bc9;color #2/C:84 #53597e;color #2/C:85 #165ad8;color #2/C:86 #9d888d;color #2/C:87 #d04dab;color #2/C:88 #b1d5ba;color #2/C:89 #c66dab;color #2/C:90 #44a151;color #2/C:91 #df5760;color #2/C:92 #66df6f;color #2/C:93 #cf1dd8;color #2/C:94 #a269ab;color #2/C:95 #551fba;color #2/C:96 #e4a7c9;color #3/A:1 #1f5c8b;color #3/A:2 #a68a40;color #3/A:3 #5f3140;color #3/A:4 #76147c;color #3/A:5 #9d5140;color #3/A:6 #6c8ed6;color #3/A:7 #37804f;color #3/A:8 #8edb31;color #3/A:9 #7b64e5;color #3/A:10 #ab2140;color #3/A:11 #a89a40;color #3/A:12 #b53231;color #3/A:13 #7e247c;color #3/A:14 #6125d6;color #3/A:15 #a2265e;color #3/A:16 #97bd7c;color #3/A:17 #aa556d;color #3/A:18 #a9a140;color #3/A:19 #9c3931;color #3/A:20 #9e407c;color #3/A:21 #8faa6d;color #3/A:22 #166f8b;color #3/A:23 #9bd97c;color #3/A:24 #76dad6;color #3/A:25 #cd90e5;color #3/A:26 #2628d6;color #3/A:27 #97ce31;color #3/A:28 #e2c07c;color #3/A:29 #933a4f;color #3/A:30 #cf328b;color #3/A:31 #a27e5e;color #3/A:32 #b5ca31;color #3/A:33 #946222;color #3/A:34 #8f546d;color #3/A:35 #28a040;color #3/A:36 #ab4740;color #3/A:37 #8c1b6d;color #3/A:38 #95946d;color #3/A:39 #d63b6d;color #3/A:40 #76ba5e;color #3/A:41 #b5524f;color #3/A:42 #8880d6;color #3/A:43 #b3ae8b;color #3/A:44 #9acd31;color #3/A:45 #77924f;color #3/A:46 #2cc0d6;color #3/A:47 #a9a340;color #3/A:48 #e2867c;color #3/A:49 #b5b431;color #3/A:50 #498e4f;color #3/A:51 #64627c;color #3/A:52 #85188b;color #3/A:53 #e4827c;color #3/A:54 #1f1a6d;color #3/A:55 #a4a27c;color #3/A:56 #cdb2e5;color #3/A:57 #60a45e;color #3/A:58 #7d2d40;color #3/A:59 #80c45e;color #3/A:60 #444422;color #3/A:61 #7ddb40;color #3/A:62 #688240;color #3/A:63 #1fbfd6;color #3/A:64 #46c05e;color #3/A:65 #71584f;color #3/A:66 #2686d6;color #3/A:67 #353ce5;color #3/A:68 #c85b8b;color #3/A:69 #a37a31;color #3/A:70 #3518e5;color #3/A:71 #4882d6;color #3/A:72 #b55631;color #3/A:73 #74487c;color #3/A:74 #6149d6;color #3/A:75 #282c40;color #3/A:76 #211e8b;color #3/A:77 #22978b;color #3/A:78 #7998e5;color #3/A:79 #a66c40;color #3/A:80 #501931;color #3/A:81 #15dd7c;color #3/A:82 #ca756d;color #3/A:83 #3b94e5;color #3/A:84 #262cd6;color #3/A:85 #7fc322;color #3/A:86 #a88840;color #3/A:87 #2b7a8b;color #3/A:88 #486cd6;color #3/A:89 #994031;color #3/A:90 #71ce31;color #3/A:91 #3a8440;color #3/A:92 #ffffff;color #3/A:93 #a2c25e;color #3/A:94 #cf968b;color #3/A:95 #28c440;color #3/A:96 #7b3ee5;color #3/A:97 #6aa8d6;color #4/A:2 #977b82;color #4/A:3 #683191;color #4/A:4 #7dc8af;color #4/A:5 #768dcd;color #4/A:6 #bb16af;color #4/A:7 #1c5373;color #4/A:8 #3727a0;color #4/A:9 #d0afaf;color #4/A:10 #6cb755;color #4/A:11 #8d7c73;color #4/A:12 #26d755;color #4/A:13 #1f15be;color #4/A:14 #7e3464;color #4/A:15 #df35be;color #4/A:16 #484555;color #4/A:17 #9764cd;color #4/A:18 #84a191;color #4/A:19 #c766af;color #4/A:20 #6f9a55;color #4/A:21 #9eb9cd;color #4/A:22 #531582;color #4/A:23 #707064;color #4/A:24 #9b80cd;color #4/A:25 #d0dbaf;color #4/A:26 #3773a0;color #4/A:27 #26a155;color #4/A:28 #414855;color #4/A:29 #e267cd;color #4/A:30 #c023cd;color #4/A:31 #b18dbe;color #4/A:32 #84d991;color #4/A:33 #1fadbe;color #4/A:34 #bc63cd;color #4/A:35 #ad19dc;color #4/A:36 #6483cd;color #4/A:37 #c9deaf;color #4/A:38 #aab2dc;color #4/A:39 #59d182;color #4/A:40 #6d6055;color #4/A:41 #1cd955;color #4/A:42 #b5cba0;color #4/A:43 #e281af;color #4/A:44 #9537be;color #4/A:45 #d6b0be;color #4/A:46 #3bcf64;color #4/A:47 #2c6755;color #4/A:48 #e586cd;color #4/A:49 #e22dcd;color #4/A:50 #e29daf;color #4/A:51 #4935a0;color #4/A:52 #caccbe;color #4/A:53 #d573be;color #4/A:54 #e229cd;color #4/A:55 #b55782;color #4/A:56 #e449cd;color #4/A:57 #614a55;color #4/A:58 #9e69cd;color #4/A:59 #5f8873;color #4/A:60 #958fbe;color #4/A:61 #9e45cd;color #4/A:62 #975564;color #4/A:63 #1cdd73;color #4/A:64 #5ba291;color #4/A:65 #bedf55;color #4/A:66 #359564;color #4/A:67 #262d55;color #4/A:68 #711fa0;color #4/A:69 #505c64;color #4/A:70 #662773;color #4/A:71 #d319be;color #4/A:72 #e2a1cd;color #4/A:73 #b5cf82;color #4/A:74 #88b2be;color #4/A:75 #bb4aaf;color #4/A:76 #dc8773;color #4/A:77 #d579be;color #4/A:78 #7c9864;color #4/A:79 #9d6c91;color #4/A:80 #79cd64;color #4/A:81 #aa1adc;color #4/A:82 #ab4891;color #4/A:83 #1ca373;color #4/A:84 #8b4a73;color #4/A:85 #802daf;color #4/A:86 #d9c4cd;color #4/A:87 #c64daf;color #4/A:88 #857b64;color #4/A:89 #a26daf;color #4/A:90 #c629af;color #4/A:91 #adb1be;color #4/A:92 #5849af;color #4/A:93 #93b3a0;color #4/A:94 #48e155;color #4/A:95 #93d3a0;color #4/A:96 #dc4d73;color #4/A:97 #d53fbe;color #4/A:98 #6a4f55 These color commands take 15-16 seconds. Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

2 1

creating an annotated structure
by Melissa Jurica 30 Jun '20

30 Jun '20

Can you provide some guidelines for how one could create an annotated structure to share with colleagues? For example, I would like to annotate the cancer associated mutations of a protein, making it easy for someone to select and visualize the associated residue in a structure. Ideally, these annotations could be grouped and sorted. Even better, they could be linked to other resources. Thanks Melissa

2 2

Converting Chimera movie script
by Vid Sustar 26 Jun '20

26 Jun '20

The following bug report has been submitted: Platform: Linux-5.3.0-61-generic-x86_64-with-debian-buster-sid ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Hello! I have tried to adapt the cliping script from http://www.rbvi.ucsf.edu/chimera/data/movie-howto-mar2012/scripts/clip.cmd to work in ChimeraX (because my structure is too big, to be loaded properly in earlier Chimera) I tried to convert the old commands to the ChimeraX, but I get an error in the line "clip front -0.5 120": Expected a keyword Please advise me how to change the code to work with ChimeraX to create a movie or to simply save a series of images of cliped planes Best regards, Vid Sustar Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.py Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/dialog.py", line 150, in _qt_safe if data_format is None else " format " + StringArg.unparse(data_format.nicknames[0]))) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 365, in collated_open return func(*func_args, **func_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core_formats/__init__.py", line 48, in open return open_python_script(session, data, file_name) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 82, in open_python_script _exec_python(session, code, argv) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 59, in _exec_python exec(code, sandbox.__dict__) File "clip2.py", line 3, in <module> ModuleNotFoundError: No module named 'chimera' ModuleNotFoundError: No module named 'chimera' File "clip2.py", line 3, in See log for complete Python traceback. > ui tool show Shell /usr/lib/ucsf-chimerax/lib/python3.7/site- packages/IPython/core/history.py:226: UserWarning: IPython History requires SQLite, your history will not be saved warn("IPython History requires SQLite, your history will not be saved") > select up Nothing selected > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.py Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/dialog.py", line 150, in _qt_safe if data_format is None else " format " + StringArg.unparse(data_format.nicknames[0]))) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 365, in collated_open return func(*func_args, **func_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core_formats/__init__.py", line 48, in open return open_python_script(session, data, file_name) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 82, in open_python_script _exec_python(session, code, argv) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 59, in _exec_python exec(code, sandbox.__dict__) File "clip2.py", line 3, in <module> ModuleNotFoundError: No module named 'chimera' ModuleNotFoundError: No module named 'chimera' File "clip2.py", line 3, in See log for complete Python traceback. > open /home/user/MASTERS/Chimera_files/PythonScripts/writeMol2.py Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/dialog.py", line 150, in _qt_safe if data_format is None else " format " + StringArg.unparse(data_format.nicknames[0]))) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 365, in collated_open return func(*func_args, **func_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core_formats/__init__.py", line 48, in open return open_python_script(session, data, file_name) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 82, in open_python_script _exec_python(session, code, argv) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 59, in _exec_python exec(code, sandbox.__dict__) File "writeMol2.py", line 2, in <module> ModuleNotFoundError: No module named 'chimera' ModuleNotFoundError: No module named 'chimera' File "writeMol2.py", line 2, in See log for complete Python traceback. > help help:user > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.py Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/dialog.py", line 150, in _qt_safe if data_format is None else " format " + StringArg.unparse(data_format.nicknames[0]))) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 365, in collated_open return func(*func_args, **func_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core_formats/__init__.py", line 48, in open return open_python_script(session, data, file_name) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 82, in open_python_script _exec_python(session, code, argv) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 59, in _exec_python exec(code, sandbox.__dict__) File "clip2.py", line 4, in <module> ImportError: cannot import name 'runCommand' from 'chimerax' (unknown location) ImportError: cannot import name 'runCommand' from 'chimerax' (unknown location) File "clip2.py", line 4, in See log for complete Python traceback. > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc > open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb > select :wat 157584 atoms, 157584 bonds, 1 model selected > hide sel target a > select ~sel 37869 atoms, 34860 bonds, 1 model selected > surface sel > color (#!1 & sel) white > select ::name="OQL" 2380 atoms, 2520 bonds, 1 model selected > color (#!1 & sel) red > select ::name="ONC" 4200 atoms, 3920 bonds, 1 model selected > color (#!1 & sel) blue > select ::name="NP" 2869 atoms, 1 model selected > color (#!1 & sel) yellow > lighting flat > lighting shadows false > graphics silhouettes false > movie record supersample 3 > clip front -0.5 > wait wait requires a frame count argument unless motion is in progress > movie encode clip.mp4 bitrate 200 Movie encoding failed because no images were recorded. > close session > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc > open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb > select :wat 157584 atoms, 157584 bonds, 1 model selected > hide sel target a > select ~sel 37869 atoms, 34860 bonds, 1 model selected > surface sel > color (#!1 & sel) white > select ::name="OQL" 2380 atoms, 2520 bonds, 1 model selected > color (#!1 & sel) red > select ::name="ONC" 4200 atoms, 3920 bonds, 1 model selected > color (#!1 & sel) blue > select ::name="NP" 2869 atoms, 1 model selected > color (#!1 & sel) yellow > lighting flat > lighting shadows false > graphics silhouettes false > movie record supersample 3 > clip front -0.5 120 Expected a keyword > close session > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc > open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb > select :wat 157584 atoms, 157584 bonds, 1 model selected > hide sel target a > select ~sel 37869 atoms, 34860 bonds, 1 model selected > surface sel > color (#!1 & sel) white > select ::name="OQL" 2380 atoms, 2520 bonds, 1 model selected > color (#!1 & sel) red > select ::name="ONC" 4200 atoms, 3920 bonds, 1 model selected > color (#!1 & sel) blue > select ::name="NP" 2869 atoms, 1 model selected > color (#!1 & sel) yellow > lighting flat > lighting shadows false > graphics silhouettes false > windowsize 200 150 > copy file clip.jpg Unknown command: copy file clip.jpg > copy Unknown command: copy > save /home/user/Desktop/image1.png supersample 3 > movie record Already recording a movie > open /home/user/Desktop/gbpmovie.cxc No such file/path: /home/user/Desktop/gbpmovie.cxc > close session > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc > open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb > select :wat 157584 atoms, 157584 bonds, 1 model selected > hide sel target a > select ~sel 37869 atoms, 34860 bonds, 1 model selected > surface sel > color (#!1 & sel) white > select ::name="OQL" 2380 atoms, 2520 bonds, 1 model selected > color (#!1 & sel) red > select ::name="ONC" 4200 atoms, 3920 bonds, 1 model selected > color (#!1 & sel) blue > select ::name="NP" 2869 atoms, 1 model selected > color (#!1 & sel) yellow > lighting flat > lighting shadows false > graphics silhouettes false > movie record supersample 3 Already recording a movie > movie stop > movie record supersample 3 > movie stop > movie stop Not currently recording > close session > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc > open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb > select :wat 157584 atoms, 157584 bonds, 1 model selected > hide sel target a > select ~sel 37869 atoms, 34860 bonds, 1 model selected > surface sel > color (#!1 & sel) white > select ::name="OQL" 2380 atoms, 2520 bonds, 1 model selected > color (#!1 & sel) red > select ::name="ONC" 4200 atoms, 3920 bonds, 1 model selected > color (#!1 & sel) blue > select ::name="NP" 2869 atoms, 1 model selected > color (#!1 & sel) yellow > lighting flat > lighting shadows false > graphics silhouettes false > movie record supersample 3 > clip front -0.5 120 ; wait 120 ; movie encode clip.mp4 bitrate 200 Expected a keyword > help help:contact.html OpenGL version: 3.3.0 NVIDIA 440.100 OpenGL renderer: GeForce RTX 2060/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Micro-Star International Co., Ltd. Model: GL63 8SE OS: Ubuntu 18.04 bionic Architecture: 64bit ELF CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz Cache Size: 9216 KB Memory: total used free shared buff/cache available Mem: 31G 6.1G 18G 662M 6.6G 24G Swap: 2.0G 0B 2.0G Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:3e9b] Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:126a] Kernel driver in use: i915 PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 File attachment: clip2.cxc

3 2

chimerax label bug
by Lukas Kater 26 Jun '20

26 Jun '20

Hi ChimeraX developers, I have been tryinng to use 2dlabel to annotate some things in a movie. I have stumbled accross a number of problems: 1) creating 2 labels with the same name causes a crasH: 2dlab create ADP text "ADP state" color black size 26 bold true xpos 0.03 ypos 0.92 visibility false 2dlab create ADP text "ADP state" color black size 26 bold true xpos 0.03 ypos 0.92 visibility false

2 3

Local resolution legend
by Tetter Stephan 25 Jun '20

25 Jun '20

Dear ChimeraX Users and Developers, I manage to color my cryoEM maps by local resolution, but can't figure out how to display a scale bar of the color code. Any ideas? Or do I have to go back to Chimera for this? Thanks, Stephan

4 4

Morph cryoEM maps result
by Aritz Roa Eguiara 25 Jun '20

25 Jun '20

Dear ChimeraX team, This is probably a previously discussed topic but I have not managed to find it specifically anywhere. So I am trying to morph a couple of maps on ChimeraX using the volume morph command, but I do not get any slider as it happens with the atom model morphing (as far as I understand there is not option for that?) Also, once I do it I get a model that is called morph that if I run the movie is recorded but I cannot bounce or control any further, is it like a one time use command that then only leaves that model result of the last frame that cannot be used anymore? Best regards, Aritz

2 2

CIF writer renumbers residues
by Daniel Asarnow 23 Jun '20

23 Jun '20

Hi all, When I save a CIF from ChimeraX (while using ISOLDE), the warning "Not saving entity_poly_seq for non-authoritative sequences" is produced, and all the residues have been sequentially renumbered from 1. When there are missing residues, each segment has to be renumbered manually afterwards. Is there some way to avoid this with PDB or CIF inputs? Is it a bug? Best, -da

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Re: [chimerax-users] Antw: [EXT] Re: selection modes
by Elaine Meng 23 Jun '20

23 Jun '20

> From: "Philipp Milkereit" <Philipp.Milkereit(a)vkl.uni-regensburg.de> > Subject: Antw: Re: [chimerax-users] Antw: [EXT] Re: selection modes > Date: June 18, 2020 at 9:06:02 AM PDT > To: <meng(a)cgl.ucsf.edu> > > Hi Elaine > just a follow-up question on the Select Menu_Mode:Add, do you think it could make sense to apply this mode also to user-defined names listed in the Basic Actions window? That seems at the moment neither in ChimeraX 0.93 nor in 1.0 the case, but could be an easy way to add fast a bunch of named selections to the current selection. Also for the subtract/intersect modes that might be an interesting option? > > best wishes, > > Philipp > >>> Elaine Meng <meng(a)cgl.ucsf.edu> 18.06.2020 17:33 >>> > Hi Philipp, > I don't think there is an ISOLDE for 1.0 yet. If I look at the toolshed it says ISOLDE 1.05b "works with 0.93" > > <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde>> > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Jun 18, 2020, at 1:18 AM, Philipp Milkereit <Philipp.Milkereit(a)vkl.uni-regensburg.de> wrote: > > > > Dear Elaine, > > > > thanks for your help! > > Your example does not work for me on ChimeraX 0.93 (2020-04-03) both on a Windows and a Linux sytem. But after installing the new production version 1.0 the selection mode works indeed there on user defined selectors as expected, which is great! > > Apparently there should be also now versions of the Isolde plugin (1.0b5 ?) which are compatible with ChimeraX 1.0, so no reason anymore to stay with 0.93.. > > > > Best, > > > > Philipp > > >>> Elaine Meng <meng(a)cgl.ucsf.edu> 18.06.2020 01:15 >>> > > Hi Philipp, > > This works fine for me using the menu. For example, start ChimeraX, then: > > > > open 2gbp > > menu: Select... Structure... Secondary Structure... Strand > > menu: Select... Define Selector... (I gave it the name "mystrands") > > menu: Select... Clear > > menu: Select... Structure... Ligand > > menu: Select... Menu Mode... Add > > menu: Select... User-Defined Selectors... mystrands > > > > Now both the ligand and strands are selected. Also works if I use commands for any of those steps. When you use the menu, the corresponding commands are echoed in the Log, and it actually works by running the commands, so it doesn't make sense that commands would work and the menu wouldn't. > > > > Tested in version 1.0. > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > > > On Jun 17, 2020, at 1:11 PM, Philipp Milkereit <philipp.milkereit(a)vkl.uni-regensburg.de> wrote: > > > > > > Dear all, > > > > > > is there a way to add user-defined selectors or named selections (command: name) to the current selection by choosing them from the Menu:Select or in the Basic Actions window? Changing to Menu_Mode:Add in Menu:Select seems not to have any effect on that. I think in Chimera1 named selections still could be added to the current selection using the „append“ selection mode. At the moment adding named selections to the current selection works for me in ChimeraX just with the command line „select add“ command. > > > > > > Many thanks for your help, > > > > > > Philipp Milkereit

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Re: [chimerax-users] [Chimera-users] convert .mod to .mrc
by Elaine Meng 23 Jun '20

23 Jun '20

Dear Emmanuel Moebel, I can't think of a simple way to make an index map from IMOD meshes, only a multistep process for each mesh object. At first I misread the question and thought you said "ChimeraX" so below are steps for both Chimera and ChimeraX in case anybody might be interested. I have not tried the entire process, however. I hope this helps, Elaine =-=-= The following instructions are for Chimera: Each IMOD mesh object from the file is a surface piece. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/imod…> You can specify that surface piece in a "mask" command as "sel" (after selecting it with the mouse) and specifying input map as "ones" to create a map that has values of 1 inside, 0 outside. Then you can scale the map by using "vop scale" to multiply values by a constant (e.g. for values of 2 or 3 instead): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#scale> Maybe if you did this for multiple mesh objects you could combine the results into one map with "vop add"; not sure how well this would work. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#add> Then you can save your index map as MRC using the Volume Viewer File menu or command "volume" <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volu…> =-=-= The following instructions are for ChimeraX. Each IMOD mesh object from the file is a surface model in ChimeraX. <http://rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html> You can specify that surface model in a "volume onesmask" command to create a map that has values of 1 inside, 0 outside, then multiply values by a constant (e.g. for values of 2 or 3 instead) using "volume scale": <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#onesmask> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#scale> Maybe if you did this for multiple mesh objects you could combine the results into one map with "volume add"; not sure how well this would work. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#add> Then you can use "save" to write your index map as MRC: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 23, 2020, at 7:00 AM, Emmanuel Moebel <emmanuel.moebel(a)inria.fr> wrote: > > Dear Chimera community, > > I am visualising a tomogram segmentation with Chimera, the format of the file is .mod and has been obtained with the IMOD software. I would like to get a voxel map from it : a volume with integer values, for ex. '0' for background, '1' for membrane, '2' for filament. Output file format needs to be .mrc or .em. Is this possible to achieve with Chimera? > > Thanks in advance, > Emmanuel Moebel, PhD

1 0

select model Z-translate
by 张佳星 23 Jun '20

23 Jun '20

Dear all， How can i do select model Z-translate use mouse? like command move z distance models when i click toolbar- Right Mouse-Move model,selected one model,scroll the mouse +right mouse ,all model will zoom Many thanks for your help, Jiaxing Zhang

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Re: [chimerax-users] [Chimera-users] Structure Minimization and Molecule Movement (ChimeraX-1.0)?
by Elaine Meng 20 Jun '20

20 Jun '20

Dear Ammar, For future reference, for ChimeraX questions it is better to use the chimerax-users(a)cgl.ucsf.edu mailing list instead of this one. We announced ChimeraX on both "announce" lists, however, because we thought Chimera users would want to know about it. (1) Moving only a subset of atoms. In ChimeraX, the way to move only a subset of the models or the atoms with the mouse is to assign the mouse to move only the selected models or atoms, then select the atoms of interest, and then move them with the mouse. For example, all of the icons in the "Right Mouse" tab of the toolbar represent different modes, and clicking an icon assigns that function to the right mouse button ( = trackpad + Alt on Windows, trackpad + command key on a Mac). Click the icon that looks like a blue sphere with arrows around it to assign the right mouse button to "move selected atoms." Then dragging with the right mouse button (or trackpad equivalent) will translate the selected atoms and additionally pressing Shift will rotate the selected atoms. Right Mouse icons and what they mean: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> Similar between Chimera and ChimeraX: there are multiple possible ways to select the ligand, e.g. choosing its residue name from menu: Select... Residue... [residue name], or Ctrl-clicking on one of its atoms and then pressing the keyboard up arrow key to promote the selection to the whole residue. <http://rbvi.ucsf.edu/chimerax/docs/user/menu.html#select> <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html> Although the Right Mouse icons only assign functions to the right mouse button, with the "mousemode" command, you can assign any of these functions to any mouse button alone or in combination with modifier keys. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> (2) There is no minimize structure tool in ChimeraX currently. There are limited local "jiggling" calculations with the "tug" and "minimize" mouse modes but only for structures with only standard biopolymer residues and water, not ligands in general: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> .... and more extensive molecular dynamics capabilities with the ISOLDE plugin for refinement/modeling into density maps: <https://isolde.cimr.cam.ac.uk/what-isolde/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 20, 2020, at 6:18 PM, Ammar Jastaniah <ajasta2(a)uic.edu> wrote: > > Hi, > I am not able to find the minimize feature function in ChimeraX-1.0. Is there an equivalent to the regular Chimera version, which is to be found under Tools ==> Structure Editing ===> Minimize Structure? > > Also. Are you able to move a PDB file ligand molecule around while keeping the other receptor PDB structure stationary/in its place in ChimeraX-1.0? Once again, this is achievable in Chimera by clicking on Tools ==> Movement ===> Movement Mouse Mode. > Thank you. > Ammar

1 0

ViewDock script
by Moustafa, Ibrahim M. 19 Jun '20

19 Jun '20

Dear All, I'm trying to run ViewDock from a script using the following command in a loop: runCommand("viewdock " + filename + " AutoDock") It works fine. However, the ViewDock window remains opened after reading each file. For large number of files it is not practical to close them manually. Is there a command to close the opened ViewDock windows to add to the script? Thank you for your help. Ibrahim

3 4

RMSD command in ChimeraX
by Hrvoje Rimac 19 Jun '20

19 Jun '20

Hi, I was wondering if there is a command in ChimeraX which calculates RMSD without first aligning the ligands (analog to Chimera command "rmsd"). The problem is that the order of atoms in the two pdb files is not identical, and in Chimera (1.14) the "rmsd" command (as well as the "match" command) compares the first atom to the first atom, the second to the second etc, regardless of their type (I checked this manually), so the calculated RMSD is very high. In ChimeraX this mismatching problem is resolved, however the only command I found was the "align" command which calculates RMSD after aligning the molecules (as "match" match does in Chimera). Is there a command that would calculate RMSD without aligning the molecules? This wouldn't be a problem if I had 2 ligands to compare, but since I have more than 900, it would be very time consuming to check and correct order of all atoms. P.S. I have attached the structures of the two ligands. The RMSD values I'm getting are: Chimera "match": 4.064 Chimera "rmsd": 4.147 ChimeraX "align": 0.252 The value I should get: 0.454 Best regards, Hrvoje Rimac Hrvoje Rimac, PhD. Postdoctoral Fellow Department of Medicinal Chemistry Faculty of Pharmacy and Biochemistry University of Zagreb A.Kovačića 1, 10000 Zagreb Croatia http://www.pharma.unizg.hr/

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ChimeraX: mmcif connectivity lost in some chains; OK in Coot
by Anderson, Jacob 18 Jun '20

18 Jun '20

Dear ChimeraX team, Thank you very much for your work on this great software. We use it daily, and without which it would be extremely difficult to articulate our science. I am touching base with a problem I am having after migrating from a pdb --> mmcif format.For context, I am running ChimeraX on Ubuntu 20.04 using a fresh deb install this morning: chimerax --version UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. To be explicit, my problem is entirely reproducible. Specifically, I have a file (attached) that when opened in ccpem's Coot v0.9-pre, has all the connectivity present. However, when I switch to ChimeraX, the connectivity of some chains are lost. A good example of this contrast on chain connectivity fidelity is chain LA and LB. (photo attached). I tried reading through the ChimeraX documentation on this CIF format,<https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/mmcif/src/mmcif_guide…> but it remained not totally clear to me what is going awry in some chains but not in others. If you might have any insight on how to overcome this problem in chimerax, and allow all the chains to remain their connectivity, I would very much appreciate your thoughts/wisdom on the topic. ~Jacob [cid:0f6782e1-eb79-43db-93e8-0f8f44417fb3]

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Antw: [EXT] Re: selection modes
by Philipp Milkereit 18 Jun '20

18 Jun '20

Dear Elaine, thanks for your help! Your example does not work for me on ChimeraX 0.93 (2020-04-03) both on a Windows and a Linux sytem. But after installing the new production version 1.0 the selection mode works indeed there on user defined selectors as expected, which is great! Apparently there should be also now versions of the Isolde plugin (1.0b5 ?) which are compatible with ChimeraX 1.0, so no reason anymore to stay with 0.93.. Best, Philipp >>> Elaine Meng <meng(a)cgl.ucsf.edu> 18.06.2020 01:15 >>> Hi Philipp, This works fine for me using the menu. For example, start ChimeraX, then: open 2gbp menu: Select... Structure... Secondary Structure... Strand menu: Select... Define Selector... (I gave it the name "mystrands") menu: Select... Clear menu: Select... Structure... Ligand menu: Select... Menu Mode... Add menu: Select... User-Defined Selectors... mystrands Now both the ligand and strands are selected. Also works if I use commands for any of those steps. When you use the menu, the corresponding commands are echoed in the Log, and it actually works by running the commands, so it doesn't make sense that commands would work and the menu wouldn't. Tested in version 1.0. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 17, 2020, at 1:11 PM, Philipp Milkereit <philipp.milkereit(a)vkl.uni-regensburg.de> wrote: > > Dear all, > > is there a way to add user-defined selectors or named selections (command: name) to the current selection by choosing them from the Menu:Select or in the Basic Actions window? Changing to Menu_Mode:Add in Menu:Select seems not to have any effect on that. I think in Chimera1 named selections still could be added to the current selection using the „append“ selection mode. At the moment adding named selections to the current selection works for me in ChimeraX just with the command line „select add“ command. > > Many thanks for your help, > > Philipp Milkereit >

2 1

selection modes
by Philipp Milkereit 17 Jun '20

17 Jun '20

Dear all, is there a way to add user-defined selectors or named selections (command: name) to the current selection by choosing them from the Menu:Select or in the Basic Actions window? Changing to Menu_Mode:Add in Menu:Select seems not to have any effect on that. I think in Chimera1 named selections still could be added to the current selection using the "append" selection mode. At the moment adding named selections to the current selection works for me in ChimeraX just with the command line "select add" command. Many thanks for your help, Philipp Milkereit

2 1

Re: [chimerax-users] ChimeraX troubleshooting
by Tom Goddard 17 Jun '20

17 Jun '20

Hi Joseph, Ok, it is complaining about a ChimeraX preference file C:\Users\Joseph\AppData\Local\UCSF\ChimeraX\ui-1 that saves your last ChimeraX window size (which is used when you start ChimeraX the next time), and saves any tools you added to the Favorites menu. It is supposed to be a text file but yours somehow contains all binary 0. Could you send us that ui-1 file, then delete it, and hopefully ChimeraX will start if there are no other problems. I will open a bug report and we will look at how this happened and probably put in some code so that if a preference file is unreadable ChimeraX will still start and just warn you about the corrupted file. You will get an email about that bug report and it would help if you could reply to that email with the ui-1 file as an attachment to help us debug the problem. Tom > On Jun 17, 2020, at 2:03 PM, Joseph Chamieh <joseph.chamieh(a)umontpellier.fr> wrote: > > Dear Tom > Thank you for your answer, this is the result of what you asked for: > > C:\>"C:\Program Files\ChimeraX 1.0\bin\ChimeraX-console.exe" --debug > C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\win32\lib\pywintypes.py:2: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses > import imp, sys, os > Traceback (most recent call last): > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 193, in _run_module_as_main > "__main__", mod_spec) > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 85, in _run_code > exec(code, run_globals) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 895, in <module> > exit_code = init(sys.argv) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 502, in init > sess.ui = ui_class(sess) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 110, in __init__ > self.settings = UI_Settings(session, "ui") > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\settings.py", line 165, in __init__ > ConfigFile.__init__(self, session, tool_name, version=version) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\configfile.py", line 289, in __init__ > self._config.read(self._filename, encoding='utf-8') > File "C:\Program Files\ChimeraX 1.0\bin\lib\configparser.py", line 696, in read > self._read(fp, filename) > File "C:\Program Files\ChimeraX 1.0\bin\lib\configparser.py", line 1079, in _read > raise MissingSectionHeaderError(fpname, lineno, line) > configparser.MissingSectionHeaderError: File contains no section headers. > file: 'C:\\Users\\Joseph\\AppData\\Local\\UCSF\\ChimeraX\\ui-1', line: 1 > '\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00' > > I remain at your disposal for any further information > Best regards > Joseph > > > _____________________________________________________________________ > Joseph Chamieh, PhD, HDR > Institut des Biomolécules Max Mousseron, UMR CNRS 5247, > Université de Montpellier, > Place Eugène Bataillon, case courrier 1706, > F-34095 Montpellier Cedex 5, France > Phone: +33 4 67 14 39 20 > Fax: +33 4 67 63 10 46 > http://www.dsbc.univ-montp2.fr/recherche_en.html <http://www.dsbc.univ-montp2.fr/recherche_en.html> > http://orcid.org/0000-0003-4209-1337 <http://orcid.org/0000-0003-4209-1337> > ______________________________________________________________________ > > De : Tom Goddard [mailto:goddard@sonic.net] > Envoyé : Wednesday, June 17, 2020 7:01 PM > À : Joseph Chamieh <joseph.chamieh(a)umontpellier.fr> > Cc : chimerax-users(a)cgl.ucsf.edu > Objet : Re: [chimerax-users] ChimeraX troubleshooting > > Hi Joseph, > > To see why ChimeraX is failing to start on Windows, run it from a Windows Command Prompt as follows (two dashes in --debug) > > "C:\Program Files\ChimeraX 1.0\bin\ChimeraX-console.exe" --debug > > and send us the error message this gives. > > Tom > > > >> On Jun 17, 2020, at 1:51 AM, Joseph Chamieh <joseph.chamieh(a)umontpellier.fr <mailto:joseph.chamieh@umontpellier.fr>> wrote: >> >> Dear ChimeraX developers, >> First I would like to thank you for your wonderful job. I was looking for a software able to modelize my peptide in 3D and do all the calculations on it and I found ChimeraX yesterday, I downloaded and installed the software and directly found it as the best answer for my “problems”, however it worked in the morning and after a restarting of my laptop on midday, I was not able to start the software, so I uninstalled/reinstalled, I restarted again but since then I could not find the solution, I use an HP laptop Win 10 64 bit, I attached the dxdiag summary. >> I would appreciate it if you could help me find the solution. >> Best regards >> Joseph >> >> _____________________________________________________________________ >> Joseph Chamieh, PhD, HDR >> Institut des Biomolécules Max Mousseron, UMR CNRS 5247, >> Université de Montpellier, >> Place Eugène Bataillon, case courrier 1706, >> F-34095 Montpellier Cedex 5, France >> Phone: +33 4 67 14 39 20 >> Fax: +33 4 67 63 10 46 >> http://www.dsbc.univ-montp2.fr/recherche_en.html <http://www.dsbc.univ-montp2.fr/recherche_en.html> >> http://orcid.org/0000-0003-4209-1337 <http://orcid.org/0000-0003-4209-1337> >> ______________________________________________________________________ >> >> <DxDiag.txt>_______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

1 0

maximized on startup
by Anthony James Schaefer 17 Jun '20

17 Jun '20

Hello, Would it be possible to add an option for the ChimeraX app to be maximized on startup? I've got the window size set to 'last used' and I almost always maximize ChimeraX. With this combo, ChimeraX starts out the size of my screen, but not maximized. Thanks, Tony

2 4

operation (rotation and translation) marix relative to the original PDB
by Steve Chou 17 Jun '20

17 Jun '20

Dear ChimeraX developers and users, After we load a 3D molecule [model (pdb) or map (mrc)] into ChimeraX, we turn (rotate) and move (translate) the molecule to find out a nice orientation to print the image. How to write out and read in the operation/manipulation matrix (rotation matrix, 3x3; translation vector, 3x1; or their combination, 4x4) relative to the original orientation/coordinates in ChimeraX? Many thanks in advance! Steve -- Steve Chou

2 1

ChimeraX troubleshooting
by Joseph Chamieh 17 Jun '20

17 Jun '20

Dear ChimeraX developers, First I would like to thank you for your wonderful job. I was looking for a software able to modelize my peptide in 3D and do all the calculations on it and I found ChimeraX yesterday, I downloaded and installed the software and directly found it as the best answer for my problems, however it worked in the morning and after a restarting of my laptop on midday, I was not able to start the software, so I uninstalled/reinstalled, I restarted again but since then I could not find the solution, I use an HP laptop Win 10 64 bit, I attached the dxdiag summary. I would appreciate it if you could help me find the solution. Best regards Joseph _____________________________________________________________________ Joseph Chamieh, PhD, HDR Institut des Biomolécules Max Mousseron, UMR CNRS 5247, Université de Montpellier, Place Eugène Bataillon, case courrier 1706, F-34095 Montpellier Cedex 5, France Phone: +33 4 67 14 39 20 Fax: +33 4 67 63 10 46 <http://www.dsbc.univ-montp2.fr/recherche_en.html> http://www.dsbc.univ-montp2.fr/recherche_en.html <http://orcid.org/0000-0003-4209-1337> http://orcid.org/0000-0003-4209-1337 ______________________________________________________________________

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Re: [chimerax-users] ChimeraX markers to IMOD model
by Tom Goddard 17 Jun '20

17 Jun '20

Hi Joe, I made ChimeraX able to read IMOD model files (same as in Chimera), in the current ChimeraX daily build. This does not help with your problem of marking particles for subtomogram averaging. As I added IMOD model reading I looked at whether ChimeraX could write such a file. The file has Fortran binary records and while I could write a file that ChimeraX would read, I am not sure whether IMOD or any other software would read it because the file has lots of information and I don't know what is required and what is optional. Tom > On Jun 17, 2020, at 7:35 AM, Atherton, Joseph <joseph.atherton(a)kcl.ac.uk> wrote: > > Thanks Tom > > Dr Joe Atherton > Lecturer in Cryo-electron Microscopy > Randall Centre for Cell and Molecular Biophysics > King's College London, UK > Email: joseph.atherton(a)kcl.ac.uk <mailto:joseph.atherton@kcl.ac.uk> > Tel: (+44) 0207 836 5454 > https://kclpure.kcl.ac.uk/portal/joseph.atherton.html <https://kclpure.kcl.ac.uk/portal/joseph.atherton.html> > From: Tom Goddard <goddard(a)sonic.net> > Sent: 16 June 2020 17:54 > To: Atherton, Joseph <joseph.atherton(a)kcl.ac.uk> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] ChimeraX markers to IMOD model > > Hi Joe, > > Neither Chimera nor ChimeraX can write IMOD model files. (Chimera can read those files but that is not available in ChimeraX yet.) So I don't know how you could get ChimeraX markers (which are written as an XML .cmm file) into an IMOD model. > > Tom > > >> On Jun 16, 2020, at 7:04 AM, Atherton, Joseph <joseph.atherton(a)kcl.ac.uk <mailto:joseph.atherton@kcl.ac.uk>> wrote: >> >> Hi, >> >> I'd like to use the markers function in ChimeraX to make an IMOD 'model' for use in PEET for subtomogram averaging. ChimeraX's 'planes' function makes it a convenient program for doing this. Is such an export/conversion possible? >> >> All the best, >> Joe >> >> Dr Joe Atherton >> Lecturer in Cryo-electron Microscopy >> Randall Centre for Cell and Molecular Biophysics >> King's College London, UK >> Email: joseph.atherton(a)kcl.ac.uk <mailto:joseph.atherton@kcl.ac.uk> >> Tel: (+44) 0207 836 5454 >> https://kclpure.kcl.ac.uk/portal/joseph.atherton.html <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fkclpure.k…>_______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl…>

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ChimeraX markers to IMOD model
by Atherton, Joseph 16 Jun '20

16 Jun '20

Hi, I'd like to use the markers function in ChimeraX to make an IMOD 'model' for use in PEET for subtomogram averaging. ChimeraX's 'planes' function makes it a convenient program for doing this. Is such an export/conversion possible? All the best, Joe Dr Joe Atherton Lecturer in Cryo-electron Microscopy Randall Centre for Cell and Molecular Biophysics King's College London, UK Email: joseph.atherton(a)kcl.ac.uk Tel: (+44) 0207 836 5454 https://kclpure.kcl.ac.uk/portal/joseph.atherton.html

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Re: [chimerax-users] ChimeraX does not start after installation
by Tom Goddard 15 Jun '20

15 Jun '20

Hi Józef, OpenGL provides no mechanism for an applications to choose among multiple GPUs, or even know that multiple GPUs are available. It is up to your operating system to choose the GPU. Tom > On Jun 15, 2020, at 10:59 AM, Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk> wrote: > > Hi Tom, > > Thanks. This is weird because I have recently updated to the latest NVidia drivers, which should have fixed this (and it didn't). I have been searching around based on your pointers and I suspect that Windows somehow tells ChimeraX to use the integrated graphics rather than one of the four NVidia GPUs (I guess Intel graphics is the GPU default in the Win installation) I have never checked or tried to update the driver for the integrated graphics so it might be that it is using some ancient generic driver (I just assumed that Windows would automatically directed ChimeraX to the more powerful GPU options). > I have found some instructions to force ChimeraX to use NVidia GPUs so I will try this (when I can access my workstation again). > > Best, > Józef > From: Tom Goddard <goddard(a)sonic.net> > Sent: Monday, June 15, 2020 5:46 PM > To: Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] ChimeraX does not start after installation > > Hi Józef, > > The reason ChimeraX does not start on hour Windows computer is given in the middle of this error message: > > ERROR: ChimeraX requires OpenGL graphics version 3.3. > Your computer graphics driver provided version 1.1 > > Your OpenGL graphics driver is not working. Version 1.1 is from the 1990s and is what Windows gives you when you have no working graphics driver. So the fix will be to install a working graphics driver. > > When ChimeraX does not get a usable graphics driver it is supposed to still start and present a message explaining this. I am not sure why it crashed in your case. But I see in your error message > > Windows fatal exception: code 0x80000003 > > and searching online this says you have misconfigured Windows system files. All the top hits when searching for that error look like scams telling you how to use their special utility to "fix" your system. Be cautious -- I would not suggest running any spacial "cleaner" tools as they are usually malware. > > > Tom > >> On Jun 14, 2020, at 9:54 AM, Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk <mailto:J.R.Lewandowski@warwick.ac.uk>> wrote: >> >> Hi Tom, >> >> I finally got to run ChimeraX-console with --debug (did not have access to the machine during lockdown) to see why ChimeraX does not start on my system. I am pasting the output below message. Can you give me any pointers on how to make my ChimeraX installation to work. From a cursory look it seems there is a problem with OpenGL implementation. >> Any tips would be welcome. I had latest Nvidia studio drivers, now I updated to the latest Nvidia gaming drivers and the problem with starting ChimeraX persists. >> >> Thanks, >> Józef >> >> Starting main interface >> [15380:7256:0608/122433.144:ERROR:gl_surface_wgl.cc <http://gl_surface_wgl.cc/>(391)] wglCreatePbufferARB not available. >> [15380:7256:0608/122433.144:ERROR:gl_surface_qt.cpp(200)] Requested OpenGL implementation is not supported. Implementation: 1 >> Windows fatal exception: code 0x80000003 >> >> Thread 0x000010d4 (most recent call first): >> File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 1139 in do_handshake >> File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 870 in _create >> File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 423 in wrap_socket >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1422 in connect >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 966 in send >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1026 in _send_output >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1247 in endheaders >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1298 in _send_request >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1252 in request >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1319 in do_open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1362 in https_open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 503 in _call_chain >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 543 in _open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 525 in open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 222 in urlopen >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\available.py", line 37 in load >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 444 in reload_available >> File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 870 in run >> File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 926 in _bootstrap_inner >> File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 890 in _bootstrap >> >> Thread 0x00001c4c (most recent call first): >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 879 in _populate_menus >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 458 in __init__ >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 196 in build >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 617 in init >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 895 in <module> >> File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 85 in _run_code >> File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 193 in _run_module_as_main >> ERROR: ChimeraX requires OpenGL graphics version 3.3. >> Your computer graphics driver provided version 1.1 >> Try updating your graphics driver. >> Traceback (most recent call last): >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\graphics.py", line 56, in event >> self._check_opengl() >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\graphics.py", line 76, in _check_opengl >> self._check_for_bad_intel_driver() >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\graphics.py", line 86, in _check_for_bad_intel_driver >> if r.opengl_vendor() == 'Intel': >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\graphics\opengl.py", line 980, in opengl_vendor >> return GL.glGetString(GL.GL_VENDOR).decode('utf-8') >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\OpenGL\platform\baseplatform.py", line 415, in __call__ >> return self( *args, **named ) >> File "src\errorchecker.pyx", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError >> OpenGL.error.GLError: GLError( >> err = 1282, >> description = b'invalid operation', >> baseOperation = glGetString, >> cArguments = (GL_VENDOR,) >> ) >> Windows fatal exception: access violation >> >> Thread 0x000010d4 (most recent call first): >> File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 929 in read >> File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 1071 in recv_into >> File "C:\Program Files\ChimeraX 1.0\bin\lib\socket.py", line 589 in readinto >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 267 in _read_status >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 306 in begin >> File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1344 in getresponse >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1322 in do_open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1362 in https_open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 503 in _call_chain >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 543 in _open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 525 in open >> File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 222 in urlopen >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\available.py", line 37 in load >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 444 in reload_available >> File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 870 in run >> File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 926 in _bootstrap_inner >> File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 890 in _bootstrap >> >> Current thread 0x00001c4c (most recent call first): >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 702 in rapid_access_shown >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 203 in build >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 617 in init >> File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 895 in <module> >> File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 85 in _run_code >> File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 193 in _run_module_as_main >> >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Thursday, March 12, 2020 9:37 PM >> To: Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk <mailto:J.R.Lewandowski@warwick.ac.uk>> >> Cc: chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> >> Subject: Re: [chimerax-users] ChimeraX does not start after installation >> >> Hi Józef, >> >> Try starting ChimeraX from a Windows Command Prompt with the debug option >> >> "c:\Program Files\ChimeraX\bin\ChimeraX-console.exe" --debug >> >> and you will probably get a Python traceback which will give some clue as to what is going wrong. If your graphics driver is not functioning ChimeraX is supposed to show you a window with an error message, but perhaps this has not been tested on Windows. >> >> Tom >> >> >> >>> On Mar 12, 2020, at 3:17 AM, Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk <mailto:J.R.Lewandowski@warwick.ac.uk>> wrote: >>> >>> Hi, >>> >>> I am trying to get ChimeraX on a Windows 10 installation on a workstation with 4 GPUs (RTX 2080Ti). >>> The program installs just fine but when I start it, it shows the splash screen up to Loading main interface and then quits. I have tried both with the 0.92 release and the daily_build. >>> Any chance you could help with with getting it to work? >>> Browsing archives I learned that this may be down to some incompatibilities with drivers. >>> The onboard graphics is ASPEED Graphics Family with driver version 9.0.10.102 >>> The four Nvidia GeForce RTX2080Ti have driver 26.21.14.4219 installed (I updated to the latest drivers hoping it fixes it - it doesn't). >>> Any ideas or suggestions? >>> >>> Thanks, >>> Józef >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

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Re: [chimerax-users] ChimeraX does not start after installation
by Tom Goddard 15 Jun '20

15 Jun '20

Hi Józef, The reason ChimeraX does not start on hour Windows computer is given in the middle of this error message: ERROR: ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.1 Your OpenGL graphics driver is not working. Version 1.1 is from the 1990s and is what Windows gives you when you have no working graphics driver. So the fix will be to install a working graphics driver. When ChimeraX does not get a usable graphics driver it is supposed to still start and present a message explaining this. I am not sure why it crashed in your case. But I see in your error message Windows fatal exception: code 0x80000003 and searching online this says you have misconfigured Windows system files. All the top hits when searching for that error look like scams telling you how to use their special utility to "fix" your system. Be cautious -- I would not suggest running any spacial "cleaner" tools as they are usually malware. Tom > On Jun 14, 2020, at 9:54 AM, Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk> wrote: > > Hi Tom, > > I finally got to run ChimeraX-console with --debug (did not have access to the machine during lockdown) to see why ChimeraX does not start on my system. I am pasting the output below message. Can you give me any pointers on how to make my ChimeraX installation to work. From a cursory look it seems there is a problem with OpenGL implementation. > Any tips would be welcome. I had latest Nvidia studio drivers, now I updated to the latest Nvidia gaming drivers and the problem with starting ChimeraX persists. > > Thanks, > Józef > > Starting main interface > [15380:7256:0608/122433.144:ERROR:gl_surface_wgl.cc <http://gl_surface_wgl.cc/>(391)] wglCreatePbufferARB not available. > [15380:7256:0608/122433.144:ERROR:gl_surface_qt.cpp(200)] Requested OpenGL implementation is not supported. Implementation: 1 > Windows fatal exception: code 0x80000003 > > Thread 0x000010d4 (most recent call first): > File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 1139 in do_handshake > File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 870 in _create > File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 423 in wrap_socket > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1422 in connect > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 966 in send > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1026 in _send_output > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1247 in endheaders > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1298 in _send_request > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1252 in request > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1319 in do_open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1362 in https_open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 503 in _call_chain > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 543 in _open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 525 in open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 222 in urlopen > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\available.py", line 37 in load > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 444 in reload_available > File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 870 in run > File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 926 in _bootstrap_inner > File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 890 in _bootstrap > > Thread 0x00001c4c (most recent call first): > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 879 in _populate_menus > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 458 in __init__ > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 196 in build > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 617 in init > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 895 in <module> > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 85 in _run_code > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 193 in _run_module_as_main > ERROR: ChimeraX requires OpenGL graphics version 3.3. > Your computer graphics driver provided version 1.1 > Try updating your graphics driver. > Traceback (most recent call last): > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\graphics.py", line 56, in event > self._check_opengl() > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\graphics.py", line 76, in _check_opengl > self._check_for_bad_intel_driver() > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\graphics.py", line 86, in _check_for_bad_intel_driver > if r.opengl_vendor() == 'Intel': > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\graphics\opengl.py", line 980, in opengl_vendor > return GL.glGetString(GL.GL_VENDOR).decode('utf-8') > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\OpenGL\platform\baseplatform.py", line 415, in __call__ > return self( *args, **named ) > File "src\errorchecker.pyx", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError > OpenGL.error.GLError: GLError( > err = 1282, > description = b'invalid operation', > baseOperation = glGetString, > cArguments = (GL_VENDOR,) > ) > Windows fatal exception: access violation > > Thread 0x000010d4 (most recent call first): > File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 929 in read > File "C:\Program Files\ChimeraX 1.0\bin\lib\ssl.py", line 1071 in recv_into > File "C:\Program Files\ChimeraX 1.0\bin\lib\socket.py", line 589 in readinto > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 267 in _read_status > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 306 in begin > File "C:\Program Files\ChimeraX 1.0\bin\lib\http\client.py", line 1344 in getresponse > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1322 in do_open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 1362 in https_open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 503 in _call_chain > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 543 in _open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 525 in open > File "C:\Program Files\ChimeraX 1.0\bin\lib\urllib\request.py", line 222 in urlopen > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\available.py", line 37 in load > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 444 in reload_available > File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 870 in run > File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 926 in _bootstrap_inner > File "C:\Program Files\ChimeraX 1.0\bin\lib\threading.py", line 890 in _bootstrap > > Current thread 0x00001c4c (most recent call first): > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 702 in rapid_access_shown > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 203 in build > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 617 in init > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 895 in <module> > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 85 in _run_code > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 193 in _run_module_as_main > From: Tom Goddard <goddard(a)sonic.net> > Sent: Thursday, March 12, 2020 9:37 PM > To: Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] ChimeraX does not start after installation > > Hi Józef, > > Try starting ChimeraX from a Windows Command Prompt with the debug option > > "c:\Program Files\ChimeraX\bin\ChimeraX-console.exe" --debug > > and you will probably get a Python traceback which will give some clue as to what is going wrong. If your graphics driver is not functioning ChimeraX is supposed to show you a window with an error message, but perhaps this has not been tested on Windows. > > Tom > > > >> On Mar 12, 2020, at 3:17 AM, Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk <mailto:J.R.Lewandowski@warwick.ac.uk>> wrote: >> >> Hi, >> >> I am trying to get ChimeraX on a Windows 10 installation on a workstation with 4 GPUs (RTX 2080Ti). >> The program installs just fine but when I start it, it shows the splash screen up to Loading main interface and then quits. I have tried both with the 0.92 release and the daily_build. >> Any chance you could help with with getting it to work? >> Browsing archives I learned that this may be down to some incompatibilities with drivers. >> The onboard graphics is ASPEED Graphics Family with driver version 9.0.10.102 >> The four Nvidia GeForce RTX2080Ti have driver 26.21.14.4219 installed (I updated to the latest drivers hoping it fixes it - it doesn't). >> Any ideas or suggestions? >> >> Thanks, >> Józef >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

1 0

Support
by greene＠chem.ucsb.edu 15 Jun '20

15 Jun '20

Hello, I am using the new ChimeraX, and it is great thus far! One issue I have come across is that if I want to display sidechains that are directly adjacent a connective line links the alpha carbons that I can't seem to get rid of. Tried lots of little workarounds, but can't seem to get it to go away (see attached picture). Is this just a bug I will have to deal with or is there a workaround? Brandon Greene *Assistant Professor * *Department of Chemistry and Biochemistry* *University of California Santa Barbara*

2 1

cut-through session color
by Steve Chou 15 Jun '20

15 Jun '20

Dear ChimeraX developers and users, Is it possible to define the color surface cut-through sessions? Thanks in advance! Steve -- Steve Chou

2 2

Cupy dependency for ChimeraX bundle
by Arthur Ecoffet 09 Jun '20

09 Jun '20

Hi, I am currently trying to develop a bundle for ChimeraX and the methods implemented can both run on GPU (using Cupy with a Cuda dependency) or on CPU. I am wondering how to deal with this "pseudo-dependency" with cupy, since it is not necessary to run the code but it is more computationally efficient. If a Cupy dependency is written in the "bundle_info.xml" file, will it create errors for computers without Nvidia Cuda installed ? Is there any way for users to install supplemental package by hand directly in chimeraX python as it was possible with Chimera ? Or is the only solution to add by hand a dependency line in the xml file ? Thanks, Arthur

3 2

Volume series
by Kotaro TANAKA 08 Jun '20

08 Jun '20

Hi, I'm trying to create a morphing movie of a series of 3D maps. For that purpose, if I understand correctly, I need a volume series (vseries) of those maps, and according to the documentation (https://www.rbvi.ucsf.edu/chimerax/docs/user/trajectories.html#vseries) I should obtain a volume series simply by opening the maps at once in a file opening dialogue. I attached a screen shot of the Models panel after opening my maps, and my question is, are those maps already consisting a volume series? vseries commands fail with 'No volume series specified' I would appreciate your comments, thank you Best regards, Kotaro

4 7

Deleting regions of whole protein
by Anas Hussain 08 Jun '20

08 Jun '20

Hello, I am currently working on a projectpertaining to the Corona Virus. I was wondering if there is anyway I could delete parts of awhole protein using the ChimeraX software. Thank you, Dr. Anas Hussain.

2 1

mesh grid sampling
by Steve Chou 08 Jun '20

08 Jun '20

Dear ChimeraX developers and users, I'm trying to display a map as mesh in ChimeraX, but the grid sampling is too sparse. *volume #1 style mesh level 0.02 step 1 color blue* Is there a way to increase the grid sampling, so that the chicken wires look denser? Thanks in advance! Steve -- Steve Chou

2 2

developing bundles autocompletion
by Daniel Esteban Palma Igor 05 Jun '20

05 Jun '20

Hi, normally I use spyder for writing python code, is there a way to have autocompletion of functions and modules when developing a bundle for ChimeraX? Any other tips for development is well received. Regards, Daniel Palma Igor

2 3

2D and 3D objects
by Jazzar, Rodolphe 04 Jun '20

04 Jun '20

Hi, First of all, this is a great program, and I am barely using it to full extent of its possibilities. I am currently interested in combining a 3D object (a molecule.pdb) and a 2D object/plane/image (as a .png or any other). The idea being that I want to show a slice of an ELF plot, with the 3D molecule embedded through the 2D plot. Good news is that I can import both objects (.pdb and .png). However I face a size issue with the 2D object, which is considerably bigger than the 3D one. Would you know if I can size down a 2D object, or enlarge a 3D one respectively. All in all would you know if chimeraX can generate something like the picture attached by combining a 2D and a 3D object. Thanks for your time, Cheers, Rodolphe [cid:D31DAF51-91B8-4F78-94B3-4C0FCD9C860E] Dr. Rodolphe Jazzar, CNRS Research Associate - (French National Centre for Scientific Research) UCSD-UMI 3555 ORCID : 0000-0002-4156-7826 Office: (858)-534-5315 Mobile: 858-337-2228 University of California, San Diego, 5213 Pacific Hall, Department of Chemistry, 9500 Gilman Dr, # 0343, La Jolla, CA 92093-0343 http://bertrandgroup.ucsd.edu<http://bertrandgroup.ucsd.edu/> https://northamerica.cnrs.fr<https://northamerica.cnrs.fr/> http://www.cnrs.fr/en/cnrs [cid:image001.png@01CFDE12.00855770]

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Re: [chimerax-users] ChimeraX cross links
by Elaine Meng 04 Jun '20

04 Jun '20

> On Jun 4, 2020, at 1:25 AM, Dina Schneidman <duhovka(a)gmail.com> wrote: > > Hi, > We are getting addicted to the ChimeraX graphics, amazing! > I couldn't find how to add cross-links on top of the structure. What would be the best way to do this? > Also, is there a way to color different cross-link types in distinct colors? > Thanks and stay safe! > Dina Hi Dina, Glad you like it, and I certainly hope you and your family are staying safe too! As I understand it there are two ways for atomic structures with crosslinks to be shown in ChimeraX: (1) some integrative modeling structures include such crosslinks. If you download the "cif" from the PDB IHM site <https://pdb-dev.wwpdb.org/> and then change its filename suffix to "ihm" instead, then you can open it in ChimeraX. If the IHM model has crosslinks, they should show up somewhere in the model hierarchy of that data, which you can explore in the Models panel. An example of one with crosslinks is the BBSome: <https://pdb-dev.wwpdb.org/entry.html?PDBDEV_00000018> (2) or if you just have any atomic structure already in ChimeraX and you want to add crosslinks, you can read in pseudobond file (filename.pb), which is just a series of atom-pair specifications in plain text. You can also include color, radius, number of dashes. The file description is the bottom section of this page: <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html> Also, you can change colors, number of dashes, and radius of any pseudobonds already in the structure or previously added, just using the commands "color" "style" and "size"; see the links in the top section of the pseudobonds page. There is a chimerax mailing list CC-d here for questions (unless they contain private data). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Installation of ChimeraX in Centos 7
by Gaya Yadav 01 Jun '20

01 Jun '20

?Dear Sir/Madam, I am trying to install Chimera X in the Centos 7 in my local directory. I installed it by converting it chimerax-rc.cpio?. But I cannot launch it, it was showing error about the openGL. Is that because of the openGL or it is not installed properly? Here is the error: WARNING: QXcbConnection: XCB error: 145 (Unknown), sequence: 178, resource id: 0, major code: 139 (Unknown), minor code: 20 NOTE: available bundle cache has not been initialized yet ERROR: ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.4 Try updating your graphics driver. WARNING: The X11 connection broke: No error (code 0) XIO: fatal IO error 0 (Success) on X server "localhost:12.0" after 668 requests (668 known processed) with 0 events remaining. ? Thanks Gaya

2 2

Source Code
by Dario Eltzner 29 May '20

29 May '20

Hello, I was interested in reading the ChimeraX source code but found only this site https://www.cgl.ucsf.edu/chimerax/docs/devel/conventions.html which references a git repo that is password protected. Is the source code not freely available? Best Wishes Dario Eltzner

2 2

Re: [chimerax-users] 3D stereo lighting is not the same as mono
by Tom Goddard 27 May '20

27 May '20

Try "camera sbs" and see if shadows look right. If they do look ok, but stereo does not then it will require some debugging with a stereo system that reproduces the problem and I am not able to test that until quarantine is over. Tom > On May 26, 2020, at 10:01 AM, Kenneth Satyshur <kenneth.satyshur(a)wisc.edu> wrote: > > Thanks. I will check out the versions as they come out. Hopefully this can be fixed. I can try a VR and see what is up with the display if anything. > kas > > > Kenneth A. Satyshur, M.S., Ph.D. > Senior Scientist, > Department of Bacteriology: College of Ag and Life Sciences; > Departments of Bio Molecular Chemistry, > Neuroscience, Oncology, and Carbone Cancer Center: > School of Medicine and Public Health; > and the School of Pharmacy > University of Wisconsin-Madison > Madison, Wisconsin, 53706 > 608-215-5207 > From: Tom Goddard <goddard(a)sonic.net> > Sent: Tuesday, May 26, 2020 11:48 AM > To: Kenneth Satyshur <kenneth.satyshur(a)wisc.edu> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] 3D stereo lighting is not the same as mono > > I made a bug report for this > > https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/3315 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/3315> > > I am not able to test stereo, don't have a computer that can do it. For me other two eye modes like VR and SBS (side-by-side) have correct shadows. The problem may be a graphics driver bug effecting shadow calculation. Or it might be a bug in ChimeraX in how OpenGL quad-buffering are used. > > Tom > > >> On May 23, 2020, at 4:39 PM, Kenneth Satyshur <kenneth.satyshur(a)wisc.edu <mailto:kenneth.satyshur@wisc.edu>> wrote: >> >> I am using version 1.0 in Centos7 with Nvidia 3D glasses and K4000 video card. I do all my work in 3D stereo. Especially density fitting. I noticed that the lighting is different in mono vs stereo mode. When i go to stereo mode with >> >> camera stereo >> >> the image is in stereo but the "full" lighting is on and the image is very dark with shadows. If I switch to 'simple' it is bright and has weak shadowing. Switching to 'soft' the image is flat black and can only be seen with white background but contains no atoms. I think this is a bug. >> But a Great improvement in rendering of images. >> thanks >> kas >> p.s. old chimera does stereo very well on my system >> Linux kenworkathome 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux >> >> >> Kenneth A. Satyshur, M.S., Ph.D. >> Senior Scientist, >> Department of Bacteriology: College of Ag and Life Sciences; >> Departments of Bio Molecular Chemistry, >> Neuroscience, Oncology, and Carbone Cancer Center: >> School of Medicine and Public Health; >> and the School of Pharmacy >> University of Wisconsin-Madison >> Madison, Wisconsin, 53706 >> 608-215-5207 >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

2 3

3D stereo lighting is not the same as mono
by Kenneth Satyshur 26 May '20

26 May '20

I am using version 1.0 in Centos7 with Nvidia 3D glasses and K4000 video card. I do all my work in 3D stereo. Especially density fitting. I noticed that the lighting is different in mono vs stereo mode. When i go to stereo mode with camera stereo the image is in stereo but the "full" lighting is on and the image is very dark with shadows. If I switch to 'simple' it is bright and has weak shadowing. Switching to 'soft' the image is flat black and can only be seen with white background but contains no atoms. I think this is a bug. But a Great improvement in rendering of images. thanks kas p.s. old chimera does stereo very well on my system Linux kenworkathome 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, Department of Bacteriology: College of Ag and Life Sciences; Departments of Bio Molecular Chemistry, Neuroscience, Oncology, and Carbone Cancer Center: School of Medicine and Public Health; and the School of Pharmacy University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207

2 1

Recreating views
by Martin Montgomery 22 May '20

22 May '20

Hi, I have a session file that contains everything I need to make figures for a paper. With pymol, I saved the get_view matrix in a text file for each view which meant that with one session file I could easily recreate the views if I needed to go back and tweak a figure. In ChimeraX, the closest way that I found to replicate this was to use named views. Am happy to supply a session file if it helps also happy to be educated if there is a better way of doing this, especially as now the ChimeraX session files can get rather large. Cheers MGM Martin G Montgomery Senior Scientist ATP Synthase Group MRC Mitochondrial Biology Unit University of Cambridge The Keith Peters Building Cambridge Biomedical Campus Hills Road Cambridge Great Britain CB2 0XY www.mrc-mbu.cam.ac.uk <http://www.mrc-mbu.cam.ac.uk/>

5 6

Save/restore scene?
by Oliver Clarke 20 May '20

20 May '20

Hi ChimeraX-ers, Is there currently an equivalent of the "scene" command from Chimera? It was super helpful to be able to quickly switch between different (and often complex) representations of a molecule. I know the view command for saving and restoring orientations, and the "name" command for saving selections, but I can't find an equivalent of scene. I'm guessing it's not yet implemented, but count me as one vote for porting it over after 1.0 is out the door, it was super helpful in Chimera! Cheers Oli

2 1

Feature suggestion - show color code in picker?
by Oliver Clarke 19 May '20

19 May '20

Hi, I love the color editor in ChimeraX, it is much nicer than the one in Chimera and is super useful! One minor suggestion - would it be possible to add a dynamically updated label showing in the editor the current color code? This sometimes shows up in the log but not always, and it is useful to have easily copy-able for use in scripts and aliases. Cheers Oli

3 4

Cartoon smooth loops chimX
by Dominik Hrebík 19 May '20

19 May '20

Hi all! Is there any possibility to smooth loops in cartoon representation in ChimeraX? I can't find it in the user guide. Something similar to pymol's cartoon_smooth_loops,1: https://pymolwiki.org/index.php/Cartoon_smooth_loops Best, Dominik -- ################################## Dominik Hrebik Laboratory of Structural Virology CEITEC, Masaryk University Kamenice 5 / A35 Brno, 625 00, Czech Republic Phone: +420 549 49 7764 <%2B420%20549%2049%207756> ##################################

2 1

Focus in ChimeraX
by Luca Pellegrini 18 May '20

18 May '20

Hi, What is the ChimeraX equivalent to the Focus command in Chimera? I have selected a portion of a structure, and would like to bring it into focus without dragging it into view. Also Focus would automatically set the selection as the pivot point. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA lp212(a)cam.ac.uk

3 2

Turntable rotation
by Scott, Brandon L. 16 May '20

16 May '20

I would like to create an animation where the camera is spun around at a constant azimuthal angle so the object appears to spin on a tabletop. Currently, when I use roll, when it spins to the backside I see underneath the model rather than remaining on top. Any help is greatly appreciated. -Brandon ____________________ Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor SDSMT, Nanoscience and Nanoengineering

3 4

Re: [chimerax-users] transition from Chimera
by Tom Goddard 15 May '20

15 May '20

Hi Jerome, Putting that "open instructions,html" in your startup preferences is a nice way to show an HTML interface that could have links that execute commands in ChimeraX. I had not thought of that use. Tom > On May 15, 2020, at 1:37 AM, MUTTERER Jerome (IBMP) <jerome.mutterer(a)ibmp-cnrs.unistra.fr> wrote: > > Hi Tom, > Thank you very much for your answers. > I didn't try the drag and drop emulation approach, but I confirm the "remotecontrol rest" option at startup works nicely. > I added the following 2 lines to the Favorites>Settings...>Startup tab > > remote rest start port xxxxx > open instructions.html > > and it makes it easy to operate. > Thanks a lot! > > Jerome > > > De: "Tom Goddard" <goddard(a)sonic.net> > À: "MUTTERER Jerome, IBMP" <jerome.mutterer(a)ibmp-cnrs.unistra.fr> > Cc: chimerax-users(a)cgl.ucsf.edu > Envoyé: Mardi 12 Mai 2020 20:14:39 > Objet: Re: [chimerax-users] transition from Chimera > > Hi Jerome, > > We don't have the chimerax --send option to open files in an already running ChimeraX, although we plan on adding it. > > I have two ideas for how to do this in current ChimeraX. One is to use the remotecontrol command to tell ChimeraX to accept commands via http. In ChimeraX I enable this with command > > remote rest start port 58123 > > Then http requests can run commands in ChimeraX. The http url can be entered in a web browser or from a script. From a script you could use curl or wget programs, for example, > > curl http://localhost:58123/run?command=open+/Users/goddard/Downloads/ChimeraX/P… <http://localhost:58123/run?command=open+/Users/goddard/Downloads/ChimeraX/P…>.cif > > You could make ChimeraX alway enable http requests by putting the "remote..." command in ChimeraX Settings/Preferences under the Startup tab "Execute these commands at startup". > > The other idea I have is simpler but did not work in my test. ChimeraX accepts files dragged and dropped on the application. On macOS (and probably Linux and Windows) I should be able to run a shell command that says drop this file on ChimeraX. On Mac the shell command looks like > > % open -a /Applications/ChimeraX.app ~/Downloads/ChimeraX/PDB/1a0m.cif > > That worked for starting ChimeraX and showing the first file. But when I run it again to open a different it merely raised ChimeraX and did not open the new file. That is a bug. I've made a bug report for it. I don't know the equivalent commands on Linux and Windows and whether the would work. > > Tom > > > On May 12, 2020, at 1:50 AM, Jerome Mutterer <jerome.mutterer(a)ibmp-cnrs.unistra.fr <mailto:jerome.mutterer@ibmp-cnrs.unistra.fr>> wrote: > > Dear all, > I'm trying to transition from Chimera to ChimeraX, but my workflow relies on passing scripts to an open, with GUI, instance of Chimera using --send > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send> > > I see that this is not described here: > https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html <https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html> > > Is that still available somehow in ChimeraX? > Thanks for any input. > Sincerely, > Jerome. > > -- > Jerome Mutterer > CNRS - Institut de biologie moléculaire des plantes > 12, rue du Général Zimmer > 67084 Strasbourg Cedex > www.ibmp.cnrs.fr <http://www.ibmp.cnrs.fr/> > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

1 0

Stuck on one XML-RPC command
by Mungo Carstairs (Staff) 14 May '20

14 May '20

Any XML-RPC fans who can help me with this please? This label command works in the PyMOL command line: label 4zho//A/36/CA 4zho//B/36/CA, "hello world" How do I format an equivalent XML-RPC request? I've tried <methodCall> <methodName>label</methodName> <params> <parameter> <value>4zho//A/36/CA 4zho//B/36/CA</value> </parameter> <parameter> <value>"hello world"</value> </parameter> </params> </methodCall> but get back a fault response XML message with <class 'SyntaxError'>:invalid syntax (<string>, line 1) I have also tried encoding the " as %22, or omitting the quotes, same result. Any ideas please? Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

1 0

Stereo and VR support
by Gökhan Tolun 13 May '20

13 May '20

Hi, Would it be possible to make the graphics window undockable, too, Like the other ones? This would allow the use of stereo monitors with SBS and tb support, which does not work currently with menus, etc. surrounding the graphics window. Also, will you implement DTI stereo as in Chimera? By the way, if theres a way of making ISOLDE work in VR, thatd be great! Thanks, Gökhan

3 3

pyqtchart
by Anthony James Schaefer 13 May '20

13 May '20

Hello, I'm interesting in using pyqtchart (https://pypi.org/project/PyQtChart/) as an alternative to matplotlib for some plots in my bundle (I like the default style better, it resizes better - small things like that). If I list pyqtchart as a dependency in my bundle_info.xml like ... <Dependencies> <Dependency name="pyqtchart"/> </Dependencies> ... a new version of PyQt5 gets installed in the directory where bundles get installed. The QChart module from pyqtchart gets installed in this new PyQt5 package. I can't use the QChart module because it's not in the PyQt5 that ChimeraX uses. Is there anything I can do with my bundle to get it to install a usable pyqtchart? Thanks, Tony

2 3

wrong version in download
by Christine Gee 13 May '20

13 May '20

Dear ChimeraX I downloaded what was supposed to be chimeraX 0.5 from your site, and 0.1 instead. I have an older mac with an older OS (10.11.6) and would like the last version that was developed for it. Can you please let me know where I can download 0.5? Also does it work with isolde? Regards Christine Dr Christine Gee Research Specialist Kuriyan Lab HHMI/Molecular and Cell Biology/QB3 527 Stanley Hall MC 3220 University of California, Berkeley Berkeley, CA 94720-3220 Lab Phone: 510 643 0164 Cell: 510 230 7891 Email: christinelgee(a)berkeley.edu <mailto:christinelgee@berkeley.edu>

2 1

Manual segmentation in ChimeraX
by Pattana Jaroenlak (Michael) 13 May '20

13 May '20

Hello, I saw the twitter post from ChimeraX on segmentation of EM serial images ( https://twitter.com/ucsfchimerax/status/1260425173238415360?s=12) It was very beautiful. I have serial section EM images. I am wondering that can I do manual segmentation on ChimeraX? Some cellular features on my images can not be picked up by thresholding or watersheding. Thank you PJ -- *Pattana (Michael) Jaroenlak, PhD* Bhabha & Ekiert Labs Skirball Institute of Biomolecular Medicine New York University School of Medicine *Email: pattana.jaroenlak(a)nyulangone.org <pattana.jaroenlak(a)nyumc.org>, p.jaroenlak(a)gmail.com <p.jaroenlak(a)gmail.com>*

2 1

Renaming chain IDs
by Fahrenkamp, Dirk 12 May '20

12 May '20

Hi ChimeraX team. I am happily using chimeraX along with ISOLDE for modelling. Lately, I am running into issues with complexes having too many chains to be handled by the standard .pdb format which is why I am using .cif now. Is there a smooth way/command to rename chain IDs and change _entity.pdbx_description _struct_asym.entity_id accordingly? Thanks! Kind regards, Dirk -- Dr. rer. nat. Dirk Fahrenkamp UKE Hamburg Zentrum für experimentelle Medizin Institut für Struktur- und Systembiologie/ CSSB Centre for Structural Systems Biology c/o Deutsches Elektronen-Synchrotron DESY Notkestraße 85, Building 15 3.OG D-22607 Hamburg Telefon:+49 (0) 40 8998-87657 Dirk.Fahrenkamp(a)cssb-Hamburg.de www.cssb-hamburg.de

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transition from Chimera
by Jerome Mutterer 12 May '20

12 May '20

Dear all, I'm trying to transition from Chimera to ChimeraX, but my workflow relies on passing scripts to an open, with GUI, instance of Chimera using --send https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send I see that this is not described here: https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html Is that still available somehow in ChimeraX? Thanks for any input. Sincerely, Jerome. -- Jerome Mutterer CNRS - Institut de biologie moléculaire des plantes 12, rue du Général Zimmer 67084 Strasbourg Cedex www.ibmp.cnrs.fr

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Map "Blobs" tool - Generate objects?
by Christophe Leterrier 11 May '20

11 May '20

Hi, I started using ChimeraX for visualization and quantification of 3D microscopy images. The "blob" tool is particularly impressive to semi-automatically segment objects of interest and measure their characteristics. However, I could not find a way to generate an independent object from the picked blobs. This makes the quantification process unreproducible as it is not possible to store the blobs in the session or automatically measure all the picked blobs. Am I wrong in the intent of the tool, or is there a way to do this? Thank you, -- Christophe Leterrier NeuroCyto lab INP CNRS UMR 7051 Aix Marseille University, France

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ChimeraX on Twitter
by Tom Goddard 08 May '20

08 May '20

For ChimeraX news, tips, tricks and special features meet us on Twitter @UCSFChimeraX. https://twitter.com/UCSFChimeraX <https://twitter.com/UCSFChimeraX> Tom, Eric, Elaine, Greg, Conrad, Scooter, Tom -- the UCSF ChimeraX team.

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How to display crystal packing?
by Guillaume Gaullier 08 May '20

08 May '20

Hello, Today I was trying to display a crystal packing from a PDB entry in ChimeraX, but could not find how to do this. I read the documentation for the sym command https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html ; but either I didn’t get it, or this is not the adequate command for what I am trying to do. What I want to do is the equivalent of PyMOL’s "Action / generate / symmetry mates / +/- one unit cell and within… Å", which is different from the biological assembly the sym command can generate from the PDB annotation. When working with crystallographic data, ISOLDE displays molecules related to the working model by crystallographic symmetry, so displaying the crystal packing seems doable in ChimeraX. Or is it one of ISOLDE’s additions? It would be wonderful if someone could help me with this (it is one of the last few things I need on a regular basis, that I still don’t know how to do in ChimeraX). Thank you in advance, Guillaume

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preview ChimeraX 1.0!
by Elaine Meng 07 May '20

07 May '20

The ChimeraX 1.0 (!!) release candidate is now available: <http://www.rbvi.ucsf.edu/chimerax/download.html> Please, please try it out and report any issues that you find, as we plan to make the production release by the end of the month. To report issues, use the ChimeraX menu: Help... Report a Bug <http://www.rbvi.ucsf.edu/chimerax/docs/contact.html> For what's new, see the Change Log: <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Problems with making movie in chimerax
by Nandish Kumar Khanra 07 May '20

07 May '20

Hello all, I want to make a movie of a multi-domain protein between two functional states using Chimerax. One domain undergoes drastic conformational change while there is virtually no structural change in another domain. I did the following steps to make the movie. * Aligned two models using matchmaker, mm #1 to #2 pair ss ss false * make morph morph #1,2 frames 100 play false cartesian true * make movie movie record size 1000,1000 coordset #3 wait 100 movie encode output ~/Desktop/movie1.mp4 quality higher framerate 25 roundTrip true The stationary domain of two functional states aligned perfectly after structural alignment, but I do see motions in that domain in the movie. Am I doing anything wrong? Is there a way to overcome this? Thanks, Nandish

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Script to color zone a map according to the underlying model
by Caroline Stone 07 May '20

07 May '20

Dear All, As an exercise in scripting, I am trying to write a script to imitate the appearance a published figure (from Toropova et al 2017). I would like to display a semi-transparent map which has been color zoned to match the underlying model in surface view. ChimeraX does everything in the script apart from the last two commands, in which I color zone the map, and then make it transparent. I don't get any errors in the log to give me a clue what to change. If I omit these last two commands from the script and then make them manually from the command line after the script is finished, it works. Is there something I can change that would allow me to include the final two commands in the script? Any pointers would be much appreciated. # ChimeraX script to imitate dynein 2 tail Toropova et al 2017 figure style # Adds custom colours to the ChimeraX session # Open model and set camera view and model rotation open 6RLB windowsize 775 775 view matrix camera -0.30533,0.56038,0.76991,623.53,0.82837,-0.24247,0.50499,467.83,0.46967,0.79195,-0.39016,-7.3434 models #1,1,0,0,0,0,1,0,0,0,0,1,0 # Work with model representation surface #1 set bgColor white lighting soft graphics silhouettes true # Define custom colours color name midblue #6b80b5 color name midgreen #a0c497 color name midyellow #f9ef87 color name midtomato #f97054 color name midmagenta #a4449b # Recolour model using custom colours defined above select #1/A; color sel midblue select #1/B; color sel skyblue select #1/C; color sel midtomato select #1/D; color sel midmagenta select #1/E/F; color sel midgreen select #1/G/H; color sel lightpink select #1/I-N; color sel midyellow select clear # Open map and modify color and transparency open emdb:4918 volume #2 step 1 volume #2 level 0.0172 surface dust #2 size 10 color zone #2 near #1 distance 15 volume #2 transparency 0.75 Best wishes, Caroline

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Silhouettes cause fill
by Daniel Asarnow 06 May '20

06 May '20

Hi, Is there any way to avoid this effect where silhouettes lead to an apparent flood fill? The helix in the upper left of this clip shows what I mean: [image: image.png] I was able to work around it a bit by making the silhouettes thinner than I'd like, and aggressively supersampling. It seems severe with any silhouette width greater than 1. Thanks and best, -da

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Re: [chimerax-users] Chimera X -showing electrostatic potential
by Elaine Meng 06 May '20

06 May '20

Dear Yi Shi, The structure is nice work, and worth showing off! We are fine so far... I hope you are well too. To color a surface by electrostatic potential in ChimeraX, currently you need to use a separate program to generate the electrostatic potential map, for example the APBS web server or the DelPhi web server mentioned/linked to the Chimera tutorial here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#es…> After you generate the map (e.g. a .dx file, .phi file, or .cube file) <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume> ... then you can open it in ChimeraX and use it for coloring the protein molecular surface with the ChimeraX "color electrostatic" command: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map> If you open a .cube file it will automatically show as isosurfaces. However, you can hide the isosurfaces such as by clicking the "eye" icon in the Volume Viewer panel, and then carry on with using the coloring command as mentioned above. Of course, you need to open the protein structure and then display the protein's molecular surface first, e.g. with the "surface" command, Actions menu, or Molecule Display icon. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 5, 2020, at 7:14 PM, Yi Shi <yi.shi(a)pitt.edu> wrote: > > Dear Elaine, > > Hope this finds you, your family and colleagues safe and well. > > We have a question about Chimera X software that you and your colleagues developed. Do you know how to show the electrostatic potential using Chimera X? Do we need some external software to do this? > > BTW, the software that you developed was amazing that we really enjoy it. And thanks a million for using our Nup84 hybrid structure for the cover of your paper in Protein Science. Absolutely beautiful work! > > Thanks in advance. > Yi > > Yi Shi Ph.D. > Assistant Professor > Department of Cell Biology > Program for Integrative Systems Biology > Pitt/ CMU Program in Computational Biology > University of Pittsburgh School of Medicine > BST3 9049 > 3500 5th Avenue > Pittsburgh PA 15213 > 412-383-3242 (office) > 412-383-3243 (lab) > www.shi-lab.org

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Scroll threshold step size
by Daniel Asarnow 04 May '20

04 May '20

Hi, Is it possible to adjust the step size when using alt + scrollwheel to change the contour level? I'd like to make it coarser for RSI reasons. Thanks, -da

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ubuntu 20.04
by Hua tiger 03 May '20

03 May '20

Please create a download and install package for ubuntu 20.04 Thank you very much. John

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Chimera-Animation equivalent utility/command
by Ray Y.-R. Wang 01 May '20

01 May '20

Dear all, I have been searching for the equivalent function in ChimeraX for the Animation functionality (under Tools/Utilities) in Chimera, where we can save many checkpoints as "scenes" in one Chimera session. I am wondering whether there's a command-line equivalent thing in ChimeraX I can adapt. Thanks so much! Best, Ray

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Missing segments
by Daniel Asarnow 01 May '20

01 May '20

Hi all, When I save a CIF from ChimeraX, the missing segment pseudobonds are replaced by real (super unphysical) bonds. Can I do something about it, or is this a bug? Thanks and best, -da

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morph movie with secondary structure and dssp
by Joel Meyerson 30 Apr '20

30 Apr '20

Hi, I am making a morph between two PDB models representing two states of the same protein, and the overall secondary structure does not change much between the models. However, there is a region where the secondary structure does change. I would like to capture the secondary structure change in the morph and have a couple questions. 1. It seems the morph uses the secondary structure from PDB #1. Is there a way to use the two different secondary structure headers from the two PDBs to define the secondary structure endpoints on the morph? 2. If the above is not possible, is there a way to restrict DSSP to update only the region of interest (i.e. a residue range), and not change secondary structure throughout the molecule? Thanks, Joel

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addh and phenix
by Daniel Asarnow 24 Apr '20

24 Apr '20

Hi, Seems like with NAG glycans the addh result is incompatible with phenix real space refinement. It's easy enough to fix by deleting HD2 - the offending hydrogen - manually. I was wondering if anyone had an opinion about this, before I report a phenix bug. Error looks like: Number of atoms with unknown nonbonded energy type symbols: 5 "ATOM 2629 HD2 ASN A 362 .*. H " (4 more similar lines). Best, -da

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How to hide dashed lines?
by Steve Chou 24 Apr '20

24 Apr '20

Dear ChimeraX developers and users, I see a dashed line between an ion and a side chain when I display the side chain. Is there a way to hide the dashed line, either in command line or GUI? How to select all the atoms in residues (e.g., /A:10-100) except n, c, and o atoms? Many thanks, Steve -- Steve Chou

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displaying ribbon and tube simultaneously
by Joel Meyerson 23 Apr '20

23 Apr '20

Hi, I would like to display a model as a ribbon, but then specify a single helix to show as a tube. So far I’ve only been able to show the model either entirely as a ribbon, or entirely as tubes. Is there syntax I can use to blend the two helix styles? Thanks, Joel

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Molecular Docking problem
by Estela Fernandes e Silva 23 Apr '20

23 Apr '20

Dears, Good night! I'm starting to use SwissDock to investigate new drugs. I'm having trouble viewing “the best result” through Chimera for Web (the browser cannot be configured) In the option “Download your predictions file” I can open all the ligands through ChimeraX (my computer's desktop) at the same time. But I would like to see only one ligand at a time. Would it be possible? Best regards Estela

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deleting sidechain in ChimeraX
by Joel Meyerson 22 Apr '20

22 Apr '20

Hi, What is the command or sequence of commands which can be used to delete the sidechain on an amino acid or range of amino acids? I reviewed the ChimeraX atom spec page but could not find a way to do this. Thanks, Joel

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Problem with showing 4 Fe-4S in pdb with chimerax
by Meinan Lyu 22 Apr '20

22 Apr '20

Dear chimerax-users(a)cgl.ucsf.edu, There is a 4 Fe-S in my structure, it shows a little bit funny when I open it with chimerax. It should only have links between Fe and S, but between 2Fe shows a link line two. Do you know how to show it normally like in pymol, or remove the links between 2Fe? I really want to draw some figures in chimerax. The attached are 4 Fe-S shown in chimrax,also shown in pymol. PDB id 2WDQ is also attached, which 4 Fe-S is in /B,F,J:303. Thanks very much. Be safe and Best, Meinan Postdoc from CWRU

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shape tool in ChimeraX
by Joel Meyerson 20 Apr '20

20 Apr '20

Hi, Chimera has a “shape” command that I find quite useful. Does ChimeraX have this feature? I could not find it in the online documentation. Thanks, Joel

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Re: [chimerax-users] [EXT] Re: passing arguments to python scripts with command runscript
by Philipp Milkereit 15 Apr '20

15 Apr '20

Hi Eric, thanks for your fast help, works now as expected! Philipp Von: Eric Pettersen <pett(a)cgl.ucsf.edu> Gesendet: Mittwoch, 15. April 2020 22:19 An: Philipp Milkereit <philipp.milkereit(a)vkl.uni-regensburg.de> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Betreff: [EXT] Re: [chimerax-users] passing arguments to python scripts with command runscript Hi Philipp, In ChimeraX, the arguments will be in sys.argv — namely sys.argv[1:] since sys.argv[0] will be the name of your script file. --Eric Eric Pettersen UCSF Computer Graphics Lab On Apr 15, 2020, at 12:47 PM, Philipp Milkereit <philipp.milkereit(a)vkl.uni-regensburg.de <mailto:philipp.milkereit@vkl.uni-regensburg.de> > wrote: Dear all, in Chimera 1 it was possible to pass arguments with runscript to python scripts which could be read out there by arguments[index]. In ChimeraX I am not anymore able to read passed values using arguments[index] in python scripts called by runscript. Was that feature dismissed or was there a change in the naming? Thanks for your help, Philipp _______________________________________________ ChimeraX-users mailing list <mailto:ChimeraX-users@cgl.ucsf.edu> ChimeraX-users(a)cgl.ucsf.edu Manage subscription: <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

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passing arguments to python scripts with command runscript
by Philipp Milkereit 15 Apr '20

15 Apr '20

Dear all, in Chimera 1 it was possible to pass arguments with runscript to python scripts which could be read out there by arguments[index]. In ChimeraX I am not anymore able to read passed values using arguments[index] in python scripts called by runscript. Was that feature dismissed or was there a change in the naming? Thanks for your help, Philipp

2 1

syntax on marker and marker link placement
by Joel Meyerson 12 Apr '20

12 Apr '20

Hi, I have a question about marker and marker link syntax. Suppose model #1 has chains A and B, and that chains A and B form a homodimer where each subunit has the same residue numbering. I would like to place a marker at the midpoint between alpha-carbons of position 10 on A and 10 on B. In turn, I'd like another marker at the midpoint between position 20 on each of the two subunits. I would then like to draw a linker between the two markers. I would expect the following syntax to work, but I get an error. marker #2 #1/a,b:10@CA color yellow radius 1 marker #2 #1/a,b:20@CA color yellow radius 1 marker link #2:1,2 color yellow radius 0.5 Gives the error: Missing or invalid "position" argument: Expected 3 floats or object specifier Any suggestions on how to fix the syntax, or is there an alternative approach? Thanks, Joel

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Move Z plane backside
by Aritz Roa Eguiara 09 Apr '20

09 Apr '20

Dear ChimeraX team, I would like to ask if there is any command to move the Z plane but not the front, but the back one, while recording a movie. I am familiar with clipping, however when recording a movie it directly appears, is there any way to do the same move z but for the far plane? Thank you in advance and happy Easter, Aritz

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How to do repetitive task using Python or command line in ChimeraX?
by 이서원 09 Apr '20

09 Apr '20

Hello, I think I'm good at dealing with the previous Chimera command line, and I'm learning Python coding and ChimeraX little by little. In Chimera, I was able to apply the Chimera command to a Python script using runCommand. So, I wrote some python scripts for Chimera, such as automatically coloring or cropping maps and/or models based on the target specification list in plain text. However, I think there's no python modules like runCommand, and I don't know how to repetitively input specifications by .cxc files. (Do I have to make as many .cxc files as many as the number of the variables?) Also I tried to understand the ChimeraX developer tutorial, but I failed to import color functions on chimeraX Python Shell. (I didn't understand how to import experimental API) Is there any fancy way to create a .cxc file that executes by sequentially inputting variables in the list? Or, How to import python modules such as color functions? (https://www.cgl.ucsf.edu/chimerax/docs/devel/core/commands/user_commands.ht…) Best regards, Seowon ______________________________________________________________________________________ 이 서 원 | Selcia Seowon Lee selcia20(a)snu.ac.kr Laboratory of Molecular Imaging , Ph.D. Candidate Department of Biological Sciences, College of Natural Sciences Seoul National University, Gwanak-gu Gwanak-ro 1, Bldg105 Rm109, Seoul 08826, Korea

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How to do repetitive task using Python or command line in ChimeraX?
by 이서원 08 Apr '20

08 Apr '20

Hello, I think I'm good at dealing with the previous Chimera command line, and I'm learning Python coding and ChimeraX little by little. In Chimera, I was able to apply the Chimera command to a Python script using runCommand. So, I wrote some python scripts for Chimera, such as automatically coloring or cropping maps and/or models based on the target specification list in plain text. However, I think there's no python modules like runCommand, and I don't know how to repetitively input specifications by .cxc files. (Do I have to make as many .cxc files as there are variables?) Also I tried to understand the ChimeraX developer tutorial, but I failed to import color functions on chimeraX Python Shell. (Experimental API Is there any fancy way to create a .cxc file that executes by sequentially inputting variables in the list? Or, How to import python modules such as color functions? (https://www.cgl.ucsf.edu/chimerax/docs/devel/core/commands/user_commands.ht…) Best regards, Seowon ______________________________________________________________________________________ 이 서 원 | Selcia Seowon Lee selcia20(a)snu.ac.kr Laboratory of Molecular Imaging , Ph.D. Candidate Department of Biological Sciences, College of Natural Sciences Seoul National University, Gwanak-gu Gwanak-ro 1, Bldg105 Rm109, Seoul 08826, Korea

1 0

silhouette scaling and image dimension
by Joel Meyerson 08 Apr '20

08 Apr '20

Hi, I noticed that when I save images in ChimeraX with silhouettes on, the apparent width of the silhouette in the output image seems to scale inversely with the image dimensions. For example, these three commands give slightly different silhouette thicknesses. Images attached. save ~/Desktop/image1.png width 500 height 500 save ~/Desktop/image2.png width 1000 height 1000 save ~/Desktop/image3.png width 2000 height 2000 Is there a way to have a fixed silhouette thickness in output images? I'd also be interested to know why this happens. Thanks, Joel

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Making New Bonds between Protein & Ligand
by Gupta, Arun 08 Apr '20

08 Apr '20

Hi I followed similar " marker link " trick proposed by Tom for making new bonds between a selection of Serine residue of protein molecule with hydroxy group functionality of ligand molecule typing the below mentioned command in ChimeraX command line . marker link #1:54@OG #2:PNS@HOP1@SG radius 0.2 However, I am repeatedly getting following error. " TypeError: Cannot bond atoms in different molecules " Can you plz suggest the correct command or alternative way for making new bond between Protein & ligand molecules. Thanks Arun

2 1

Making new bonds
by Mutum YAikhombA 07 Apr '20

07 Apr '20

Hi I was trying to make new disulphide bonds between a pair of cysteine residues (say residue numbers 142 and 157) using ChimeraX. The standard Chimera command - 'bond' doesn’t work in ChimeraX. I have gone through the structure editing tool and couldn’t find an equivalent tool. I found some command-line tools in this page (new-bond), but this seems to be not so straightforward to use - https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.htm… <https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.htm…>. Could you please help? Thanks Yaikhomba

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