August 2023 - ChimeraX-users - RBVI Mailing Lists

How to reduce subdivision of the mesh?
by HL F 29 Aug '23

29 Aug '23

Dear ChimeraX Development Team, I hope this email finds you well. First and foremost, I would like to express my heartfelt gratitude for developing such a powerful and invaluable tool like ChimeraX. Your dedication to providing the scientific community with a free and versatile platform is truly remarkable. I am writing to inquire about a technical aspect related to exporting 3D models in ChimeraX. I'm using ChimeraX-1.1.1 to export protein meshes(surface model) into Blender. I've got a problem that the mesh is too smooth which means it has too many vertices. And that makes my Blender run very slow. Is there a way to reduce the subdivision(resolution/vertex number) of the mesh in ChimeraX? Thank you very much! Looking forward to your reply. Regards, Hualing [image: image.png]

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updating session with new version of model
by Alexis Rohou 28 Aug '23

28 Aug '23

Hi there, I have a nice figure saved as a .cxs session file. But I've since had to change the PDB file to refine the model. I think myself and others have asked this in the past, and there isn't a way to substitute one PDB file for another in a ChimeraX session file. Please correct me if I'm wrong. Failing that, I have to recreate the same display style (colors, ribbon vs sticks vs balls, etc) with the new PDB file. What I was thinking of doing is to save a series of files containing attributes' values from the original model (with option ModelId set to false), and then open these files back and read the attribute values into the new model. Things like display, draw_mode, color, ribbon_display, ribbon_color, etc. In principle, do you think this approach should work? One stumbling block: I can't seem to save the display attribute. Specifically, the following command: > save browse format defattr attrName a:display models #1 modelId false Gives the following output in the log: > One or more attribute values aren't integer, floating-point, string or > None (e.g. False); skipping those > Saved attribute 'display' of 0 atoms using match mode: 1-to-1 to > <filename_redacted> This is with version 1.6.1 (2023-05-09). I have tried with other attributes (e.g. draw_mode), and they seemed to work. What is the correct way to save the atom display attribute to file? Cheers, Alexis

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How allow a plugin to save a startup setting
by BARRY E DEZONIA 28 Aug '23

28 Aug '23

Hello, I am developing a plugin. One attribute my plugin has is an output directory. I want to save that value somewhere so that if you exit chimerax, come back in, and reload my plugin the output directory value will default to what it was during the last run, I've read a bit about session data and preference data and I don't think they get at what I want. I might be able to make my app save a data file in the installed plugin directory (and read it on startup) but maybe there will be things like permissions issues trying to do something like this. Any suggestions on how to do what I want to do?

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Re: [Chimera-users] Atlocs
by Elaine Meng 28 Aug '23

28 Aug '23

Hi Hernando, ChimeraX has an Altloc Explorer tool (also implemented as "altlocs" command) that lists all the residues with alt locs and allows switching which ones are used: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/altlocexplorer.html> The rules that ChimeraX uses for deciding which ones to show initially are described in that link, namely: "For each contiguous (through-bond) set of atoms with alternate locations, the location used initially is that with the highest average atomic occupancy, then as a tie-breaker, the lowest average atomic B-factor, and if a tie-breaker is still needed, by alphabetical order of the alternate location ID." We found that altloc A is not always the most occupied! So yes, this is a new feature of ChimeraX, but we also added the tool to make it easy to switch if you want to use a different altloc than what is shown initially. By the way: You may be interested that there is a chimerax-users(a)cgl.ucsf.edu list (CC'd here) specifically for asking questions about ChimeraX. Since ChimeraX and Chimera are two different programs with different behaviors, we try to somewhat separate the questions so that people won't get too confused! 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 28, 2023, at 12:38 PM, Hernando J Sosa via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear ChimeraX, > > I have an atomic model with several chains that have residues with alternate locations A and B. I noticed that > while Chimera by default displays alternate locations A. ChimeraX for some chains display alternate locations A and for other chains alternate locations B. Why is this behavior different in Chimera and ChimeraX? Is this a novel feature of ChimeraX? I this is the case how ChimeraX decides which of the two alternate locations A or B to display? > > Thanks > > Hernando

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consult
by UehkVt 27 Aug '23

27 Aug '23

Hi, I am using ChimeraX on Linux OS.I think ChimeraX only has a single-line command window which isn't convenient for complex script. I want to know there are other ways to type multiple-line command and display protein structure whin ChimeraX at real time. could Jupyter notebook combine with ChimeraX? When we type command in Jupyter notebook, ChimeraX could display the result of the command.Could you tell me the method that can solve the above issue? Thanks! Sincerely!

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General developer questions
by BARRY E DEZONIA 25 Aug '23

25 Aug '23

Hello, I have been writing a plugin for ChimeraX. One feature it does now is read a PDB file, parse some info, and act on that data internally. I'd like to change it so that it can use information about a loaded PDB in ChimeraX. To this I have a couple questions: 1. Are there some basic docs on how someone could access a protein that is memory resident that was loaded from a PDB (i.e. just what data structures can I access programmatically related to a protein loaded with open(<pdbname>)). 1. How do I find the data structure(s) for the currently viewed or selected or ??? protein? I'd like someone to be viewing a protein and then launch my plugin which will use that protein and its data for the plugin's internal calculations. I'm sorry if this is noise. If there are good developer docs for these topics please feel free to point me in the right direction. Thanks.

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How to use ColorBrewer palette?
by Tianyang Liu (Staff) 25 Aug '23

25 Aug '23

Hello, I would like to colour my structure with the ColorBrewer palette using ChimeraX. But I can't seem to get it to work. I used the command: color bychain cartoons;palette Pastel1-9. The error message displayed is "Unknown command: palette Pastel1-9." Could you help me with this please? Many thanks, Tian

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Does getcrd return coordinates in pixels or in angstroms?
by Samuel Haysom 25 Aug '23

25 Aug '23

Hello, I am trying to determine the coordinates of a point on a volume for use in cryoSPARC (as described here for Chimera: Job: Local Refinement (Legacy) - CryoSPARC Guide<https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/loca…>). I was wondering if the getcrd command returns coordinates in angstroms (as it did in Chimera) or whether they are in pixels? This was not specified on the getcrd documentation page as far as I could see (Command: getcrd (ucsf.edu)<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/getcrd.html>). KR, Sam Samuel Haysom | Research Scientist | Biophysics Sosei Heptares | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

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Changing Colors and Unable to Save as pdb File
by Natalia Tegenfeldt 25 Aug '23

25 Aug '23

I have been using chimerax to visualize the proteins I'm working with, and have been highlighting sections of the sequence and changing the color to highlight those sections, but when I try to save it as a pdb, it gets rid of the colors. Is there a different way to be able to keep a section highlighted/different color when I save it as a pdb file? Thanks!

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Question on Chemistry StackExchange regarding ChimeraX Python Log.
by nikolic＠uwm.edu 24 Aug '23

24 Aug '23

Hello, I'm developing a series of commands and presets for ChimeraX and run into the following trouble in self-support: https://chemistry.stackexchange.com/q/175802/136866 Thank you! Nickolas Nikolic

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