- ChimeraX-users - RBVI Mailing Lists

Mapping local correlation between two maps
by Reza Khayat 06 Dec '17

06 Dec '17

Hi, Chimera allows one to map the CC between two maps onto a map and color the surface using the following commands: vop localCorrelation #0 #1 scolor #0 volume #2 cmap 0.6,red:0.7,white:1,blue I'm having difficulty executing the second command -mapping the values onto the first volume and assigning colors. Any help would be appreciated. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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activate model selectively
by Gabor PAPAI 29 Nov '17

29 Nov '17

Dear ChimeraX developers, I have a very naive question: how can I activate models selectively, like in Chimera? I would like to superimpose a density map with a pdb, but I don’t find how I can only activate and move the pdb. Thank you in advance for your help! Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

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VR and optional functions
by Matthias Wolf 26 Oct '17

26 Oct '17

Hi Tom et al, Great job on chimeraX! The rendering engine is incredible. I have tried to view our cryo-EM volumes in VR with a new HTC Vive – it’s amazing and it works really well! ChimeraX supporting VR was one of the reasons for me to buy the Vive. Thank you! Now I haven’t used chimeraX before (I have used chimera since many years). I understand that the program is still work in progress. However, I am really missing some of the nice functions of chimera that make it so useful with a “clicky” interface - e.g. color surface by radius or by pdb properties, segmented isocontoured maps, clipping planes, subvolumes, combined shaded and wireframe surfaces, biological assembly, etc – I find these functions very useful and there don’t seem to exist any command line options for this, or I just haven’t studied them enough yet. Many of the existing menus in chimeraX have a fraction of the functionality of their sister program chimera. E.g. volume viewer, model panel, side view – I still have not figured out how to activate only one of several objects for rotation, when in chimera a click on the activate check box in the model panel does that (there is no active checkbox in the model panel of chimeraX and I couldn’t find a command to activate an object). It would be nice if one could simply grab an object in VR and rotate by itself it instead of the entire scene. Do you have a plan to add or port some of these beloved GUI functions from chimera into chimeraX? Could they be added by copying python modules from chimera? It would be great, if one could press a button in VR on the hand controller to display the menu and select functions “by virtual laser pointer”. This could preserve the development effort that went into the GUI design of chimera by reusing it in chimeraX as an identical projected 2D menu in VR and it would prevent having to take the goggles off for simple model adjustments. Best regards, Matthias

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Re: [chimerax-users] error when save sessions of chimeraX in Ubuntu
by Elaine Meng 19 Oct '17

19 Oct '17

> On Oct 18, 2017, at 2:07 AM, Yahui Yan <yahuiuk(a)gmail.com> wrote: > > Hi Elaine, > > I am a new user of chimeraX. I run it (the daily builds on 17th Oct 2017) in my Ubuntu system. All went well until I tried to save the session. An error message '[Errno 25] Inappropriate ioctl for device' popped out. Could you please give me some advice to fix it? Many thanks. > > Kind regards, > Yahui > Hi Yahui, I don’t know the answer, but I’m sharing it to the mailing list: chimerax-users(a)cgl.ucsf.edu … that is the recommended address for ChimeraX questions. Regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Fly function in ChimeraX
by Cheng, Tat 17 Oct '17

17 Oct '17

Hi, I have trying to make movies using Chimerax. But I am not sure I can find the command "fly" in Chimerax. Is there any replacement for the "fly" command? Thanks. Tat Cheng

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no distinguishing between capital and non-captital chain IDs in morph
by Haselbach, David 16 Oct '17

16 Oct '17

Hi everyone, I am using morph with same true to interpolate between two models. Unfortunately the models have each so many chains that there are capital and non capital letters used. The problem I have is, if I want to color the chains in the morph result I cant distinguish between capital and non capital chain ids anymore. So if I do "color #10/R green" not only chain R gets green but also chain r. I guess this is a bug. But is there a workaround? Best David

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mini info
by Bruno Villoutreix 02 Oct '17

02 Oct '17

Dear Colleagues do you think chimeraX could run on mac el capitan (10.11) or it requires the version above ? many thanks Bruno -- Dr. Bruno Villoutreix, PhD Structural Bioinformatics-Molecular Medicine, Chemoinformatics DR1 Inserm Head Inserm-Paris 7 Unit U973 Therapeutic molecules in silico (MTi) Inserm U973 - Lamarck Building 35 rue Helene Brion 75013 PARIS In silico tools and databases and more in my updated website : http://www.vls3d.com <http://www.vls3d.com/>

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Feature Request: Named selections
by Jared Adolf-Bryfogle 15 Sep '17

15 Sep '17

Hi All! I just started playing around with the alpha, and I’m very happy with it so far! Really love to windows and the ability to easily select models. One thing that is missing is a similar list of selections (yes, ala PyMol). I find these to be extremely useful in a long running session and I was wondering if something like that is planned. It would be similar to the model window, where you could control each selection and maybe apply view controls to each selection as well - like having components that are cartoon and others stick, etc. Thanks for any info! Sincerely, -Jared Jared Adolf-Bryfogle, Ph.D. Research Associate Lab of Dr. William Schief The Scripps Research Institute

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Fitmap enhancements?
by Oliver Clarke 14 Sep '17

14 Sep '17

Hi, fitmap can currently sequentially fit different models, but it would be really handy if fitmap could also sequentially fit parts of an individual model (in a single fitmap command). It would be great for a quick fit of a large complex if there was an `eachChain` and maybe `eachSegment` command, to sequentially fit each chain or each contiguous stretch of polypeptide. `eachSelection` would also be useful, allowing the user to give a list of atom selections for sequential fitting in fitmap. Cheers Oli

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Color palettes - ColorBrewer support?
by Oliver Clarke 12 Sep '17

12 Sep '17

Hi, I see in the help for the “rainbow” command that there is an option for web-fetched palettes – any chance for integrating support for ColorBrewer ( http://colorbrewer2.org/#)? It has different very well-designed palettes for sequential (e.g. color by residue) divergent (e.g. color by charge or hydrophobicity) and qualitative (e.g. color by chain) data, and they are designed to be colorblind-safe etc. It’s intended for cartography, but I have manually used their palettes for structural biology with pleasing results – the full set of palettes can be downloaded as JSON or in an excel spreadsheet. Cheers Oli

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Re: [chimerax-users] [Chimera-users] 3D-SNFG symbol representation for carbohydrate molecules
by Eric Pettersen 06 Sep '17

06 Sep '17

Hi Oliver, We discussed this at the meeting today and the upshot is that we are very interested in doing this, but it will take us awhile to get to it. We intend to make a beta release of ChimeraX by the end of the year and there’s a lot of work to get done between then and now. Part of that work is to implement the “Nucleotides” representation that you see in regular Chimera but that isn’t yet available in ChimeraX. The “alternative atom depiction” that Nucleotides provides requires much of the same underlying support that showing the alternative carbohydrate depictions will require. Implementing Nucleotides first will allow us to iron out the issues involved in supplying that support and debug it. That will make implementing the 3D-SNFG representation much faster and improve its reliability. So we hope to be able to provide the carbohydrate depictions not long after the beta release date. I’d like to provide something faster, but as a practical matter I think this is the best we can do. I’m sure we will have questions about the details once we get onto the implementation, and hope you won’t mind if need to bug you a bit. :-) —Eric Eric Pettersen UCSF Computer Graphics Lab > On Aug 31, 2017, at 4:22 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > Dear Dr. Grant, > We are definitely interested, though we would be more likely to implement it in ChimeraX than Chimera, since most of our new work is in ChimeraX and also ChimeraX has better underlying support for adding new depictions like this. We will discuss this in a meeting on Tuesday and get back to you with further details. > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > >> On Aug 31, 2017, at 7:18 AM, Oliver Grant <olivercgrant(a)gmail.com <mailto:olivercgrant@gmail.com>> wrote: >> >> Dear developers, >> >> The carbohydrate community has decided on a standard symbol representation for carbohydrates. The article is here <https://academic.oup.com/glycob/article-lookup/doi/10.1093/glycob/cwv091>, and the webpage is here <https://www.ncbi.nlm.nih.gov/books/NBK310273/>. Our group has created a 3D version <http://glycam.org/docs/othertoolsservice/2016/06/03/3d-symbol-nomenclature-…> of the symbols within the software VMD. Here's a video showing both versions. <http://glycam.org/docs/othertoolsservice/wp-content/uploads/sites/15/2016/0…> We have also worked with David Sehnal to implement this into LiteMol, here is an example <https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/?loadFromCS=5a6z>. I wanted to reach out and see if you are interested to implement this representation within Chimera? We can discuss the details if so. >> >> Regards, >> >> Dr. Oliver Grant >> Associate Research Scientist >> Complex Carbohydrate Research Center >> Athens, GA, USA. >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Not a software whiz!!!!!!!!!
by Arthur Szabo 05 Sep '17

05 Sep '17

Have downloaded ChimeraX as I would like to include a ribosome structure or part of it in my work. ChimeraX is, I am aware, largely a command based operational process. I feel like a real dummy because I do not understand how to achieve the imagery that I would like I have been able to open PDB 4WPO can rotate it and similar things, and there seem to be two molecules in the unit cell. I stumbled on a list of all the proteins, rRNAs and some other components in the structure such as EFG, an elongation factor. Can't figure out how to delete one of the model units from the image, as I was able to do with Chimera. I find it virtually impossible to understand the logic of the commands. Of course the command structure is similar to that in Chimera, but I only used that infrequently. I used the menu driven tools etc almost exclusively. I could achieve what I wanted with them and the learning curve was quite tolerable. Then when I got stuck I received excellent advice from Chimera staff on how to use the commands when needed. For example color spec<atomspec.html> colorname general-options What is the designation or meaning of spec ? How would I select the EGF protein from the ribosome to color it. 4wpo #1, chain DZ: 50S ribosomal protein L9,Elongation factor G. 4WPO is the pdb number, #1, I believe to one of the two units in the model. Chain DZ refers to the protein. I tried several permutations of this information and only received error messages. color<help:user/commands/color.html> 4wpo #1, chain BZ: 50S ribosomal protein L9,Elongation factor G Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword color<help:user/commands/color.html> red 4wpo #1, chain BZ: 50S ribosomal protein L9,Elongation factor G Expected one of 'atoms', 'bonds', 'cartoons', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword color<help:user/commands/color.html> ribbons red 4wpo #1, chain BZ: 50S ribosomal protein L9,Elongation factor G Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword color<help:user/commands/color.html> ribbons red 4wpo #1, chain BZ Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword Colorname I think I understand, and I think that I have found a log of the different colors. Have no idea of what general-options might refer to. Here is more of my log. show<help:user/commands/show.html> selAtoms ribbons help<help:user/commands/help.html> help:user select<help:user/commands/select.html> 4wpo #1, chain BZ Expected an objects specifier or a keyword help<help:user/commands/help.html> help:contact.html help<help:user/commands/help.html> help:contact.html color<help:user/commands/color.html> #1 BZ red Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword Similarly I can't understand what the terms in select spec<atomspec.html> [ polymer chain-spec<atomspec.html> ] might mean. The learning curve will be very much steeper than that for Chimera. Please allow me to make a suggestion. It would be useful to have a list with the definition of the terms used in the commands with clear examples. One example is spec another would be ref-spec or general-options I couldn't find one if it was there. These are only a few examples. Such terms are not defined anywhere. The persons most familiar with them are the persons who have written the programs, and those who have used the programs extensively. Some things like ( cartoon | ribbon ) atom-spec<atomspec.html> [ smooth factor | default ] [ suppressBackboneDisplay true | false ] appear to be well explained but again atom-spec is not defined nor an example given at least none that I could find. Kindly consider my comments as questions and friendly suggestions. I downloaded Pymol the other day, and couldn't get to first base. Would have to take a course on how to use it. I removed it from my computer. I don't have the time to learn even the basics about Pymol, and there are no clear explanations anywhere. I assume students learn from their colleagues who have spent considerable time learning the nuances of the program. I have a similar view of Photoshop - huge learning curve. Maybe an interactive course on YouTube video might be useful for ChimeraX Regards And thanks. AGS

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Re: [chimerax-users] Color protein by residue
by Elaine Meng 29 Aug '17

29 Aug '17

Hi Tom, Could you say more about what you mean about “collaborative” in terms of VR, what program(s) you used, how you controlled the display (e.g. typed commands to color and show/hide or something else like menus in the VR or voice control) or and whether you were looking at atomic details of proteins or just overall structures? (If you don’t want to send that info to the whole list, can just e-mail me individually.) For the most part, what we’ve done with ChimeraX is described here: <http://www.cgl.ucsf.edu/home/meng/chimerax/docs/user/vr.html> Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > > Hi Elaine, > > Wow, your .cxc file works perfectly. Thanks for showing me how to do this, great help. > > On the VR stuff, yes, I’ve been using the VR on/off with our HTC Vive system. Works great if you keep the lighting effect simple. It is why I was suggesting your team take a look at what is possible in an immersive collaboration VR environment. I look forward to hearing from someone on your team. > > Best, and again thanks, > Tom >

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Color protein by residue
by Tom Skillman 28 Aug '17

28 Aug '17

I can’t figure out the command for coloring the proteins of a protein with standard colors.. Can you help? Thx. ________________________________ --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org

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Re: [chimerax-users] 4D imaging - metadata and time slider
by Mateusz Biesaga 23 Aug '17

23 Aug '17

Hi all, I use ChimeraX for 4D visualization and so far I am very satisfied with the results, thank you for this amazing tool! I have a two questions: - While presenting data that changes in time (xyt or xyzt as I do in Chimera) it is usually required to display the timing on the image. Is there a way to access the metadata and display it, possibly using 2dlabels function? I work particularly with TIFF files. - After I upgraded Chimera to second alpha release, I can see no time slider above the command line. I open my 4D data using asterisk in the filename, as described in tutorial: http://www.rbvi.ucsf.edu/chimera/data/light-apr2017/light4d.html Is there a new way of accessing this slider? Thanks, Mateusz

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ChimeraX alpha 2 release available
by Elaine Meng 17 Aug '17

17 Aug '17

Hi everybody, Earlier this week, we made a second alpha release of ChimeraX. It’s available in the download page, along with the earlier alpha release and the ongoing daily builds. <http://www.rbvi.ucsf.edu/chimerax/download.html> To help you decide when and if to update, we’ve also created a change log listing some of the more significant changes and when they occurred. We intend to keep adding to it as development proceeds. <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> Enjoy! Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Remote control?
by Simon Smith 24 Jul '17

24 Jul '17

I'm trying to find a way to mirror ChimeraX commands from one machine onto several others running on a network. Could someone tell me if the 'remotecontrol' command would be a good way to do this, and if so, how I could get started using it? As far as I can tell there's no documentation available for it yet. Thanks, Simon

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VR Features
by Fortney, Christopher (NIH/OD/ORS) [C] 21 Jul '17

21 Jul '17

Hello Chimera X Team, My name is Chris Fortney - I run the VR Program at the NIH Library. We've been using ChimeraX for VR demonstrations here for some time now, ever since James Tyrwhitt-Drake (3D Print Exchange, NIAID) and I first installed it here earlier this year. The word has spread at NIH - people like ChimeraX for VR! I was hoping I could just email you to introduce myself, and to give feedback on the main features that have been requested. The first being the ability to make selections and then view/add labels while in VR. The second being the ability to add additional cameras to the scene. This would be especially useful for mixed reality. We have a green screen here, and would love the ability to drop a 3rd camera into the scene for that. Being able to add additional cameras could be very useful to run multiple headsets in the same scene, so that two scientists could work on the same structure at the same time. Looking forward to hearing back, keep up the excellent work! It definitely has not gone unnoticed over here. Thanks, Chris Fortney

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Tool autostart
by Eric Pettersen 19 Jul '17

19 Jul '17

You can now control which tools are auto-started when ChimeraX starts by bringing up a context menu over the tool (typically by right clicking) and toggling “Start this tool at ChimeraX startup” on/off. This works for all tools/toolbars. It’s a little tricky for the Python shell tool in that that tool’s builtin context menu is pretty handy so we didn’t want to replace it. To control that tool’s autostart you have to position the mouse on the thin border that surrounds the type-in area and bring up a context menu there. That menu will have the autostart entry in it. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Saving PDB files
by Eric Pettersen 18 Jul '17

18 Jul '17

ChimeraX can now save PDB files. See the documentation for the ‘save’ command <http://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html> for details. You can also save PDB files from the File->Save dialog, but since the dialog does not yet display the command options, they will have their default values. That may be good enough in some cases. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [chimerax-users] [Chimera-users] Is it possible to dump out the SAS surface points calculated by ChimeraX?
by Elaine Meng 10 Jul '17

10 Jul '17

Hello Francois, (There is a chimerax-users e-mail list, CC’d here.) Note that the surface displayed in Chimera and ChimeraX is the SES, not the SAS. For spacing of points, see the “surface” command option “gridSpacing” — use ChimeraX command “help surface” or view the help at our website: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#options> Use ChimeraX command “save formats” to see what formats you can save. STL or X3D would include the surface vertices, I believe. For full details on “save” use command “help save” or see the copy here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.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 Jul 10, 2017, at 2:01 AM, Francois BERENGER <berenger(a)bioreg.kyushu-u.ac.jp> wrote: > > Hello, > I am not interested by surface normals, > the 3D coordinates would be enough. > > Is it possible to control the surface sampling of the surfacing algorithm? > Like with a number of points per Angstrom^2 parameter? > Thanks a lot, > Francois. >

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H bonds
by Eric Pettersen 30 Jun '17

30 Jun '17

ChimeraX can now find hydrogens bonds. The “hbonds” command is very similar to the same command in Chimera 1. The principal difference is that since ChimeraX uses cylinders instead of lines to depict the hydrogen bonds, the “lineType” and “lineWidth” keywords have been replaced with “dashes” and “radius” (and the hydrogen bonds are now dashed by default). Full details are available with “help hbonds” or at this link: http://www.cgl.ucsf.edu/chimerax/docs/user/commands/hbonds.html <http://www.cgl.ucsf.edu/chimerax/docs/user/commands/hbonds.html> Unfortunately, the hydrogen bond computation is also slower than in Chimera 1. We are working on that. —Eric Eric Pettersen UCSF Computer Graphics Lab

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From Arun: Request for information
by Arun Prasad Chopra 23 Jun '17

23 Jun '17

Dear Sir, I was using Chimerax software to identify the residues (aminoacids and nucleotide) that are interacting and also if we can know the binding energy of this transcription factor with DNA motif. I would be thankful for helping me identifying the residues. The PDB file is enclosed Thanks and Best Regards Arun -- Arun P. Chopra, Ph.D. Associate Prof., Department of Biotechnology Hindustan College of Science and Technology, Farha, Mathura 281 122 UP, India Cell # + 921 969 7932, 956 800 6057 http://hcst.edu.in/ http://www.sgei.org/

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Cheat Sheet for ChimeraX
by Dan Echelman 20 Jun '17

20 Jun '17

Hi all, I'm just getting started on ChimeraX and was wondering if anyone had made a quick reference sheet for the commands? Thanks and best! Daniel

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Initialzing core
by Hernando J Sosa 16 Jun '17

16 Jun '17

Dear ChimeraX team, I just downloaded/installed ChimeraX (64 for windows, latest daily build & PC running Windows 7) but when starting the programs hangs with the message Initializing Core and an image of the group (Nice picture though!). Anything I should do differently? (Chimera 11.2 runs fine in the same computer). Thanks Hernando

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