- ChimeraX-users - RBVI Mailing Lists

A couple questions about programming in ChimeraX
by William Hofsøy 22 Sep '21

22 Sep '21

Hi, I'm currently working on a plugin that deals with a cmm-file model and have a few questions about how to do certain things. Mainly I would like to be able to modify the model by adding new markers and links to the model. I have managed to figure out how to make new markersets and add them to the session but not how to alter existing ones aka the model that I load from the cmm file. Additionally I am making use of the marker_extra_attributes info since the cmm file im reading has attributes there that I need, but as I read in the documentation these aren't saved in sessions and I wondered if there is a way to do just that. Lastly, I was wondering if it is possible to place any mesh in the scene, for instance a cube. -William

2 3

Re: [chimerax-users] Adding a custom preset question
by Elaine Meng 22 Sep '21

22 Sep '21

Hi Boaz, Just download the file using your standard browser mechanism. When I ctrl-click on the link "kyte-doolittle_hydrophobicity.cxc" in this page: <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup> ...when viewed in Firefox on Mac, I get a menu that includes "Save link as..." Choosing that brings up a little dialog that I use to save the file (without changing the name, but you can change it if you keep the cxc part) to my desired download location. On other platforms or different browsers it might be slightly different how to get the context menu with the choice to save the file, but should be similar. Or since it is a plain text file, like you said, you can also view contents and then paste them as plain text in a text-editor to create your own cxc file. However it is usually easy just to save the file from the browser as described above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 21, 2021, at 10:13 PM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi, > You give a nice example of adding the kyte-doolittle_hydrophobicity.cxc to the custom_presets folder that I created, but where can I find this file? Or, should I paste the content of the file which is opened by pressing the link in the user guide into a file by this name ( I doubt it but nevertheless suggest it as a possibility). > Excuse my naive question, please. > Thanks, > Boaz

1 0

color zone colors by atom type
by vincent Chaptal 21 Sep '21

21 Sep '21

Dear ChimeraX users, I just subscribed so apologies if this has been asked before. When is type the command: color zone #2 near #1/A distance 5 sharpEdges false farColor blue I have the volume #2 in blue with chain A colored by atom type: i.e. with carbons in sand, oxygens in red, nitrogens in blue. I tried to follow the tutorial on youtube, downloading the model and emdb like in the tutorial, and it does work like the tutorial, meaning colored by chain. I am wodering what is going on and how to fix it? I've seen this behavior for my protein, on a PDB refined from Phenix, or from a download from the rcsb. I don't see anything special on the PDB, all the atoms are listed normally. Is it possible to assign a specific color per chain using this command? Thank you for your help. best Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

2 3

Download Speed
by Gulzar Singh 21 Sep '21

21 Sep '21

Dear Chimera Teach team, The download speed of software is less than 200KB/s (mostly 160 KB/s). I tried both Firefox and wget. We have download limit of 11MB/s My location is Pune, India Please have a look at the issue. Regards, Gulzar Singh

2 1

Turning off silhouettes to specific selection
by Abhilash Padvannil 17 Sep '21

17 Sep '21

Hi Is there a way to turn off the silhouettes on specific selections of a model? Thanks Abhilash.

2 1

Remove older ChimeraX Linux
by Nebojsa Bogdanovic 16 Sep '21

16 Sep '21

Hello, I am trying to reinstall the new ChimeraX on the linux system, however my previous incomplete installations are creating problems. I am not sure how to get rid of them and start anew so I would appreciate your help. I can send more context in our next correspondence. Looking forward to hearing from you. Thank you and best regards. Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

2 1

Interface residue selection - command line option?
by Vorländer,Matthias Kopano 15 Sep '21

15 Sep '21

Dear ChimeraX team, I am trying to selected interface residues using the “interface” tool. While doing this through the context menu of the interface plot works, I am analyzing a larger number of PDBs and am therefore looking for a way to achieve this through the command line (the contacting chains are displayed already in the log window. Essentially I wonder if it is possible to expand this to the contacting residues). Thanks a lot in advcance, Matthias

3 4

how to save .pdb file of predicted fusion protein generated by chimerax and alphafold
by Ruby Pelingon 15 Sep '21

15 Sep '21

Hi, I tried using chimeraX and alphafold to predict my fusion protein. The result seems promising and generated a .pdb file. I would like to enquire how to save the .pdb file. I would like to open the .pdb file using pymol. Thank you. Kind Regards, Ruby Pelingon

2 2

Re: [chimerax-users] [ChimeraX] #5218: surface color value on mouseover replaced by chain info in status line
by Elaine Meng 15 Sep '21

15 Sep '21

Hi Boaz, When a bug is reported as fixed, the next successful daily build should contain the fix. Occasionally the fixer might forget to do all the steps to get it in that day, but it is supposed to be in there. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 15, 2021, at 8:14 AM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi Tom, > Thanks a lot. Is this fix already implemented in the Chimerax daily build? > Cheers, > Boaz > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben Gurion University > Beer Sheva, Israel > > On 14 Sep 2021 17:26, ChimeraX <ChimeraX-bugs-admin(a)cgl.ucsf.edu> wrote: > #5218: surface color value on mouseover replaced by chain info in status line > ----------------------------------+------------------------- > Reporter: Elaine Meng | Owner: Tom Goddard > Type: defect | Status: closed > Priority: high | Milestone: > Component: UI | Version: > Resolution: fixed | Keywords: > Blocked By: | Blocking: > Notify when closed: | Platform: all > Project: ChimeraX | > ----------------------------------+------------------------- > Changes (by Tom Goddard): > > * status: assigned => closed > * resolution: => fixed > > > Comment: > > Fixed. > > Made surface value status message suppress chain description status > messages on mouse hover. > > -- > Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5218#comment:3> > ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> > ChimeraX Issue Tracker > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

1 0

Fwd: Display of actual values of APBS electrostatic potential projected on protein surface
by Boaz Shaanan 13 Sep '21

13 Sep '21

Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel ---------- Forwarded message ---------- From: בעז שאנן <bshaanan(a)bgu.ac.il> Date: 9 Sep 2021 17:39 Subject: Display of actual values of APBS electrostatic potential projected on protein surface To: ChimeraX-users-request(a)cgl.ucsf.edu Cc: Hi, Is there a way in Chimerax to know the actual APBS electrostatic potential values in various points on the surface? Is there such feature already in Chimerax that I missed? Such feature is essential (I think) to monitor subtle changes in surface potential following mutations or other variations (pH, salt concentration etc.). If it's not there yet, could you please add it to the (enormous, I guess) to-do list? In Chimera this is done by moving the cursor to the various points of interest, a feature that I found most useful (and helpful in convincing color blind referees 😉). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

3 3

Re: [chimerax-users] Problems with Measuring Angles in ChimeraX
by Elaine Meng 10 Sep '21

10 Sep '21

> On Sep 10, 2021, at 11:41 AM, liangb2 <liangb2(a)rpi.edu> wrote: > > Hi Elaine: > I'm new to ChimeraX for Cryo-EM data. Currently, I imported my tomogram (.mrc file) into ChimeraX and acquired a density map of it. I was able to get the x,y,z coordinates of the three points of interest. However, I was not able to find ways to measure the angle among the three points on the tomogram density map. I have looked up tutorials, but all of those I have found are for proteins. > > Can you please provide some help on how I can measure the angle among three points on the density map? I would really appreciate your help. > Thank you for your time! > Best, > Biqing Liang Hi Biqing, Welcome to ChimeraX! We recommend using the chimerax-users(a)cgl.ucsf.edu address for asking questions (CC'd here so you don't need to do anything). Depending on the question, other people might want to see the answer, or give better answers than mine, or I might not know the answer at all. I don't know how you got the X,Y,Z coordinates for those three points. The way I know how to do it: You can put several "markers" (balls, fake atoms) at points on the surface, and/or at peaks in the density values. Then you can select any 3 of the markers (Shift-Ctrl-click on them) and then use the "angle" command: angle sel <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html> The way to put markers on interactively is first to go to the Markers toolbar across the top of the ChimeraX window. The different icons assign different ways of adding markers by mouse click. For example, clicking the third from left icon in the Markers toolbar assigns the right mouse button (= trackpad + Alt on Windows, trackpad + command key on Mac) to adding markers on the surface. See the following for what the different icons mean and explanation of markers: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/markers.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html> 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

Question.
by Yunsik Kang 10 Sep '21

10 Sep '21

Hello, My name is Yunsik Kang, and I am a postdoc in Marc Freeman's lab at the Vollum Institute. I would love to use ChimeraX to predict the structure of my protein of interest. I watched all the YouTube videos and tried to run the program. Unfortunately, my protein is 5005 amino acids in humans and 2958 aa in yeast. I get a message "Please use the full AlphaFold system for long sequences." My question is what is the best way to approach this problem? Should I cut the protein in half and run the program? In one of the videos, it mentions after 700 aa it will have problems. Will it work if I get Colab-Pro? Or would the server crash no matter what. I am not a structural biologist, but I hope the structure can help be predict me with my research. Thank you, Yunsik

4 7

Help with Volume Series
by Ioannis Skalidis 10 Sep '21

10 Sep '21

Greetings to all! I am trying to play a volume series data in ChimeraX (daily build). I open the multiple .mrc frames and they are automatically grouped, but then, when I use the vseries play command, I get an error message that I have not specified a volume series. What am I doing wrong? Should I open the frames differently? I also tried to open them with the open command, a wildcard character for the frame names and vseries true modifier but even then, it only opens the first frame, which I found very strange as well. Could somebody offer some advice? It would be greatly appreciated! Cheers, Yiannis. -- Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/

2 1

Re: [chimerax-users] [ChimeraX] #5198: Transparent background not transparent when selection outline shown
by Zhao, Bingchun (NIH/VRC) [F] 10 Sep '21

10 Sep '21

Hi, Tom, I received this below email reported that this bug has been fixed. Do I need to download the latest version and re-install the ChimeraX? Thank you very much! Best, Bingchun On 9/9/21, 9:35 PM, "ChimeraX" <ChimeraX-bugs-admin(a)cgl.ucsf.edu> wrote: #5198: Transparent background not transparent when selection outline shown --------------------------------------+------------------------- Reporter: bingchun.zhao@… | Owner: Tom Goddard Type: defect | Status: closed Priority: normal | Milestone: Component: Graphics | Version: Resolution: fixed | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | --------------------------------------+------------------------- Changes (by Tom Goddard): * status: assigned => closed * resolution: => fixed Comment: Fixed. Offscreen rendering was making a framebuffer with no alpha channel, even though for image save it already had an offscreen framebuffer with alpha channel. Made offscreen check and not create a new framebuffer if we are already using an offscreen framebuffer. -- Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5198#comment:3> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> ChimeraX Issue Tracker

2 2

outline the interface region in chimeraX
by Zhao, Bingchun (NIH/VRC) [F] 09 Sep '21

09 Sep '21

Hi, I wonder if there is a way to outline the interface region in ChimeraX like below: [cid:image001.png@01D7A597.5344EDF0] Previously, I did this in photoshop, but can we label the interface regions with those lines in ChimeraX? Thank you very much! Bingchun Bingchun Zhao, PhD Postdoctoral, VF Biodefense Research Section VRC/NIAID/NIH Bldg 40, Room 2607B 40 Convent Drive Bethesda, MD 20892 Tel: 301-761-7649 Email: bingchun.zhao(a)nih.gov<mailto:bingchun.zhao@nih.gov>

3 6

Re: [chimerax-users] getting AlphaFold predictions
by Elaine Meng 09 Sep '21

09 Sep '21

Hi Yk, Forwarding to chimerax-users(a)cgl.ucsf.edu since I don't have a good answer for this currently. (We prefer you use that address for questions unless they include some data that needs to stay private.) Thanks! Elaine > On Sep 9, 2021, at 1:57 PM, Yunsik Kang <kangy(a)ohsu.edu> wrote: > > > Hi Elaine, > > Thank you again! > > I did open it and using ChimeraX I can see the pdb files and see the structure! It is amazing! > > One question. > > Since my protein is massive and this is just parts of my protein, is there a way ChimeraX can stitch it all together? > > Like Tristan says it is 1400 residues each, can I perhaps somehow stitch the whole thing together? > > Yk > > -----Original Message----- > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Thursday, September 9, 2021 8:12 AM > To: Yunsik Kang <kangy(a)ohsu.edu> > Cc: meng Elaine <meng(a)cgl.ucsf.edu> > Subject: [EXTERNAL] Re: [chimerax-users] getting AlphaFold predictions > > Hi Yunsik, > I do not know the answer to your questions. We are not the developers of AlphaFold or the AlphaFold database. We only added tools in ChimeraX to connect to them. > > Maybe there is information at the AlphaFold database about what's in their download. I have never downloaded these myself. > <https://www.alphafold.ebi.ac.uk/download> > > All I know is that "tar" is a way of putting multiple files together and that you have to "untar" to get them apart. This is a standard computer file thing, not related to any specific kind of files. > > Usually if you doubleclick the tar file your computer will automatically untar it and make some new folder or folders containing the files. You would need to have enough space available on your computer for the large number of files. > > I don't know how they are named but maybe there is a README file that comes with it, or if not, you may need to look at the files with a text editor. Maybe they have the Uniprot IDs of the proteins somewhere in the names or header text of the file. > > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On Sep 8, 2021, at 7:36 PM, Yunsik Kang <kangy(a)ohsu.edu> wrote: >> >> Hi Elaine, >> >> Thank you for the fast response. My proteins are not found in the Alphafold search. >> >> I am new to this so bear with me. I downloaded the human TAR file as Tristan has said, but have no idea how to search or even start looking for my protein. >> >> Could you help? Or is this something I need professional help with? >> >> Would it help to tell you the protein I am interested in? >> >> Thank you again. >> Yunsik >> >> From: Elaine Meng <meng(a)cgl.ucsf.edu> >> Sent: Wednesday, September 8, 2021 3:44 PM >> To: Yunsik Kang <kangy(a)ohsu.edu> >> Subject: [EXTERNAL] Fwd: [chimerax-users] getting AlphaFold >> predictions >> >> Forwarding in case you did not get Tristan's reply below: >> >> >> Begin forwarded message: >> >> From: Tristan Croll via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> >> Subject: Re: [chimerax-users] getting AlphaFold predictions >> Date: September 8, 2021 at 3:17:28 PM PDT >> To: ChimeraX Users Help <ChimeraX-users(a)cgl.ucsf.edu> >> Reply-To: Tristan Croll <tic20(a)cam.ac.uk> >> >> The human protein will be in the EBI-Alphafold2 database, but not accessible to the search tool. For human proteins (and only human, so far) longer than ~2000 residues, the predictions are provided as multiple 1400-residue fragments starting at residue 1, 201, etc.. The only way to get those right now is to download the tarball of the complete set of human protein predictions, and find them in there. >> >> >> On 8 Sep 2021, at 23:08, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hi Yunsik, >> I don't know where/how you can run a prediction for such a long sequence, maybe others can comment on that. However: >> >> First make sure there is not already a predicted structure for that protein in the AlphaFold Database! E.g. try the Search button on the AlphaFold tool and see if the same UniProt entries as you are interested in are found. The database includes human and other well-studied species (maybe also the yeast you mentioned, depending on the exact species). If the prediction is already in the database, there is no need to run a new calculation. >> >> ChimeraX AlphaFold tool: >> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.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 Sep 8, 2021, at 2:45 PM, Yunsik Kang via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hello, >> >> My name is Yunsik Kang, and I am a postdoc in Marc Freeman’s lab at the Vollum Institute. >> >> I would love to use ChimeraX to predict the structure of my protein of interest. I watched all the YouTube videos and tried to run the program. >> >> Unfortunately, my protein is 5005 amino acids in humans and 2958 aa in yeast. I get a message “Please use the full AlphaFold system for long sequences.” >> >> My question is what is the best way to approach this problem? Should I cut the protein in half and run the program? In one of the videos, it mentions after 700 aa it will have problems. Will it work if I get Colab-Pro? Or would the server crash no matter what. >> >> I am not a structural biologist, but I hope the structure can help be predict me with my research. >> >> Thank you, >> Yunsik >> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> > >

1 0

Save pdb file
by Zhao, Bingchun (NIH/VRC) [F] 09 Sep '21

09 Sep '21

Hi, First, I wanna thank you for all your work to develop ChimeraX, it’s so powerful. I do have a question and would like to have your input. I opened a EM density map (.mrc) and two pdb files in chimerax (version 1.2), then fit all the pdb models into the EM map. Then, I hide the EM map, only show the pdb models after fitting, and then I would like to save these all pdb files in a new pdb file with all position information after fitting. Would you please give me any direction how to do this? I tried saving them, but only partial pdb files saved, also tried combine commend, but it said no such commend. Thank you very much! Best, bingchun Bingchun Zhao, PhD Postdoctoral, VF Biodefense Research Section VRC/NIAID/NIH Bldg 40, Room 2607B 40 Convent Drive Bethesda, MD 20892 Tel: 301-761-7649 Email: bingchun.zhao(a)nih.gov<mailto:bingchun.zhao@nih.gov>

2 2

error saving a surface
by Diego Amaya 08 Sep '21

08 Sep '21

Hi, I'm running a python script in --nogui and --script mode and I'm getting an error when doing rc(session, 'save surface.stl format stl'). The error message is : *QGuiApplication::font(): no QGuiApplication instance and no application font set.Segmentation fault* I'm working with debian 10 and I used the production release 1.2.5-1 Thanks in advance for the help. -- Diego A. Amaya Ramírez -- *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.

2 2

capture reply from run(session, command)
by Sean Connell 08 Sep '21

08 Sep '21

Hello I was wondering if it is possible to capture the output that goes to the log when you run the python command run(session, command). For example if I run: run(session, "mmaker #2/A to #1/A”) Can I store in a variable the reply in the log file that has information about the RSMD? Sean

2 2

distance between centers of mass using python API
by Diego Amaya 08 Sep '21

08 Sep '21

Hello, I'm trying to compute the distance between the centers of mass of two residues using the python API. I tried two different ways : 1. *rc(session, 'define centroid :43 massWeighting true name AA1')rc(session, 'define centroid :35 massWeighting true name AA2')rc(session, 'distance AA1 AA2') * 2. *rc(session, ' measure center :43 mark true name AA1')rc(session, 'measure center :35 mark true name AA2')rc(session, 'distance AA1 AA2')* But I get this error in the third line in both cases : *chimerax.core.errors.UserError: Missing or invalid "objects" argument: invalid objects specifier * What is wrong ? Thanks in advance. -- Diego A. Amaya Ramírez -- *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.

2 5

Question about use of ChimeraX
by Jonathan Choong 07 Sep '21

07 Sep '21

Hi there, Hope you are doing well. I just had a question regarding ChimeraX that I was hoping to get some clarity on. I was wondering whether it was possible to use ChimeraX commands (such as open, run, save) in the system command line without actually opening the application interface? Thanks, hope to hear back from you. Kind regards, Jonathan

2 1

Re: [chimerax-users] [Chimera-users] matchmaker for more than one chain
by Elaine Meng 03 Sep '21

03 Sep '21

Hi Mani, There is a different e-mail address for ChimeraX questions: it is chimerax-users(a)cgl.ucsf.edu CC'd here. Responses below... > On Sep 2, 2021, at 2:22 AM, manikandank via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi ChimeraX-users, > I have used recently the mmaker cmd to align two pdb each have multiple chains as below. > > mmaker #12/L,M,N to #5/S,A,B matrix blosum-62 showAlignment true > > But the sequence view shows only the alignment of chain L and S. > > 1. I would like to have aligned sequences of all chains used in mmaker alignement. Your command above does not use all the chains for fitting, it only chooses the single pair of chains that gives the best sequence-alignment score to superimpose the two models. The other chains might look superimposed but it is only because they moved along with the ones that were actually used for the fit. To use all three pairs of chains, you need to also use the "pairing ss" option: mmaker #12/L,M,N to #5/S,A,B matrix blosum-62 showAlignment true pair ss Then you would get three pairwise sequence-alignment windows: L/S, M/A, and N/B. matchmaker or mmaker command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> pairing options <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> > > 2. Is it possible to open the saved RMSD header values in a file later just to color the pdb? Yes, but with several steps so it may not be that convenient. Probably easier just to save and restore the ChimeraX session (which includes the sequence alignment windows). Also remember if you move the structures relative to each other, the RMSD values will change. However, if you really want to save the RMSD values to file after you showed sequence alignments and header, then you could save them as an attribute file (that could be reopened/applied later): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> The attribute name is seq_rmsd as explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers> > > 3. Do mmaker align entire pdb based on selected chains and Can calculate RMSD for all residues in the pdb? For the first question, 3A: yes, depending on the "pairing" option as explained above. For the second question, 3B, I'm not sure what you want. Remember that the main purpose of matchmaker is to superimpose the structures well, and then it happens to also give the RMSD over the positions that it chose to use, which are shown in the pinkish boxes on the sequence alignment. By default it uses fit iteration and discards loops that don't superimpose well in space. Matchmaker only gives the RMSD over the positions it uses. You could tell it to use all positions, but that would change the superposition. If you like the default superposition (that does not use all of the positions), you can use a separate command "rmsd" to measure RMSD over any sets of atoms that you want, without moving the structures or changing the superposition. Or, if you really want to use all of the positions in the sequence alignment for the fitting, you would have to use matchmaker option "cutoff none" ... but that usually does not give the best superposition. cutoff option <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#cutoffDis…> rmsd command (calculate RMSD in current positions, no fitting) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html> Matchmaker only gives alpha-carbon RMSD. The rmsd command can give RMSD for any sets of atoms that you want, alpha-carbons only, or backbone only, or all atoms, as long as you give equal numbers of atoms from the two structures. However, it can be tricky to specify the correct sets of atoms if the residue numbering or residue types are different between the two structures. So you might want to first use "mmaker" with whichever options give you the best superposition, and then to measure RMSD over all positions in the alignment (which might not be used in the matchmaker fit), use the "rmsd" command afterward. > > 4. I also would like to change the displayed text for the sequence name. Presently it puts the filename as sequence name. > > [similar to 'Edit sequence name' in the sequence viewer in chimera] Sorry, there is no way yet to change the displayed sequence name in ChimeraX. > > Please let me know how this can be done. > thank you very much > with kind regards > Mani. 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

bundle dependency not installed
by Lagerwaard, I.M. (Ilse) 02 Sep '21

02 Sep '21

Hello, I'm currently developing a bundle with a dependency on pandas. Even though I included this dependency in my bundle_info.xml file, I get "ModuleNotFoundError: No module named 'pandas'". For now, I have installed pandas on the ChimeraX console via the command prompt. For future distribution, however, it would be nice if it were immediately installed together with the bundle. I would greatly appreciate your help with this issue. Thanks in advance, Ilse

2 1

Re: [chimerax-users] output mmCIF file
by Elaine Meng 02 Sep '21

02 Sep '21

> On Aug 31, 2021, at 1:50 PM, Liu, Xiangan <Xiangan.Liu(a)uth.tmc.edu> wrote: > > Hi, > I have issue to output the models I build in pdb formation to mmCIF formation. I did not provide the sequences in orginal pdb files. Could please let me know what is the problem and how to fix it? > Thanks, > Xiangan > ---------- > File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/mmcif/__init__.py", line 89, in save > mmcif_write.write_mmcif(session, path, **kw) > File "src/mmcif_write.pyx", line 145, in chimerax.mmcif.mmcif_write.write_mmcif > File "src/mmcif_write.pyx", line 149, in chimerax.mmcif.mmcif_write.write_mmcif > File "src/mmcif_write.pyx", line 542, in chimerax.mmcif.mmcif_write.save_structure > KeyError: ('a1', 'RPGMMDSQEFS') > > KeyError: ('a1', 'RPGMMDSQEFS') > > File "src/mmcif_write.pyx", line 542, in chimerax.mmcif.mmcif_write.save_structure Hi Xiangan, We recommend using the chimerax-users(a)cgl.ucsf.edu address for questions (CC'd on this message, so you don't need to do anything this time). The address you used is just for commercial licensing. Actually, if you get a traceback like this, you can usually use ChimeraX menu: Help... Report a Bug instead of sending e-mail. You may need to attach your session file so that we can reproduce the problem. I don't know the answer, so I'm using this address to share your question with the others. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

3 3

ChineraX saves huge session files
by Dror Noy 31 Aug '21

31 Aug '21

Hi Recently, ChimeraX on my Mac (macOS Catalina) started saving very large session file. Regardless of the size of the pdb file I load - the session file is 124 MB even for small 2-3 MB pdb files. I’d appreciate any help. Thanks Dror

2 1