- ChimeraX-users - RBVI Mailing Lists

How to batch process structures?
by jacky zhao 21 Jan '20

21 Jan '20

Hi everyone, I have tried to use chimeraX yesterday. It is vey cool! I just wonder how to batch process the structures? We will generate more than thousands of structures and will analysis the binding interface. Can I use chimeraX to instantly show the interface interactions one by one? Thank you for your time. Jacky

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Exporting image in 300 DPI
by Hassan Ahmed 21 Jan '20

21 Jan '20

Hello, I wanted to ask if it is possible on ChimeraX to export image with 300 or 150 DPI? I can not find a possible selection tool as the older chimera versions. Is there a certain command or an option to do it? Thank you in advance, Regards, Ahmed -- Ahmed Hassan Institute of Plant Biology Braunschweig University of Technology Spielmannstrasse 7 38106 Braunschweig Germany Tel: +49 - 531 - 391 5885 e-mail: a-a.hassan(a)tu-braunschweig.de

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Tile a vseries
by Sean Connell 17 Jan '20

17 Jan '20

Hello, I was wondering if it is possible to tile multiple volume series such that one can have 2-3 series playing side by side? If so could you suggest the syntax for the tile command I cannot seem to get it right? I have the two vseries loaded as #1 and #2 (and each series has 10 sub volumes). I have tried variations of tile #1,2 columns 2 spacingFactor 1 and get errors like this: Traceback (most recent call last): File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", line 258, in execute cmd.run(cmd_text) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2837, in run result = ci.function(session, **kw_args) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/std_commands/tile.py", line 27, in tile spacing = max([m.bounds().radius() for m in models]) * spacing_factor File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/std_commands/tile.py", line 27, in <listcomp> spacing = max([m.bounds().radius() for m in models]) * spacing_factor AttributeError: 'NoneType' object has no attribute 'radius' AttributeError: 'NoneType' object has no attribute 'radius' File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/std_commands/tile.py", line 27, in spacing = max([m.bounds().radius() for m in models]) * spacing_factor Thanks in advance for any suggestions you have. sean

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Save scene like in "Chimera"
by Lau Kelvin 17 Jan '20

17 Jan '20

Hello all, Is there a save scene command like in chimera. I have found the command for positions via “view”. If not, its back to saving many sessions at the moment. Best, Kelvin -- Kelvin Lau https://people.epfl.ch/kelvin.lau Protein production and structure core facility - PTPSP EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin.lau(a)epfl.ch<mailto:kelvin.lau@epfl.ch> Phone: +41 21 69 30267<tel:+41%2021%2069%C2%A030267> If unreachable: +41 21 69 34494<tel:+41%2021%2069%C2%A030267>

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Show active site metal and ligand in morph
by Yifan Wang 16 Jan '20

16 Jan '20

Dear chimeraX developer, I am a graduate student from university of Texas at San Antonio. I’m trying to make a movie to compare two of my structures (resting state and substrate bound) using the function “morph”. But there is a problem, I very appreciate if you can help me figure this out. As show in Figure 1, I have two structures superposed. The resting state (nude) contains an active site metal ion coordinated by three residues and 3 water molecules. And the substrate bound (blue) also contains a metal coordinated by the same residues, a remaining water molecule, and a new ligand as my substrate. After I entered command “morph #1,2 frames 60”, I got the result of Figure 2. However, the active site metal ion and the water and substrate are missing. I want to show the active site changes between model 1 and 2. Model #3.1 seems keep the metal coordination bonds but I can’t make it present even with “show”. So my question is how to show the metal and the corresponding ligands in morph? Regards, Yifan Wang [cid:143A130E-412D-4674-AB95-99EA0C21DF44@UTSARR.NET] [cid:90E28A3D-AB8F-402F-A982-8B40682176A1@UTSARR.NET]

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Re: [chimerax-users] [Chimera-users] Chimera X commands
by Elaine Meng 14 Jan '20

14 Jan '20

Hi Drew, You may be interested that there is also a mailing list specifically for ChimeraX questions: <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> We’re glad you like Chimera! For ChimeraX we wanted to make various command-line improvements such as to make it easier to specify chains, to give several commands more obvious names or make them easier to use, etc. If you download ChimeraX the User Guide is in the Help menu, with the top page being an index of tools and commands that links to their individual pages. We also have a copy of the User Guide at our website: <http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html> The User Guide includes a page on the ChimeraX atomspec syntax and another on how it is different from Chimera’s. <http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> <http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec-diffsum.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 Jan 13, 2020, at 9:53 PM, Andrew Waight <waight(a)msg.ucsf.edu> wrote: > > Hello all, > I've been an exclusive Chimera user for over 15 years. I have been scripting a lot in python lately and am super excited to learn that ChimeraX is written in python3. I totally want to import some chimera functions into my programs. Problem is, the ChimeraX command syntax seems all new (i can't even really figure out how to select properly, is there a ChimeraX command index that I am missing and is ChimeraX for me? ChimeraX looks beautiful by the way. Thanks you guys are amazing! > Drew

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Show dashed lines after hiding atoms
by Ahmad Khalifa 09 Jan '20

09 Jan '20

How can I show the dashed lines that signifies an interruption in the structure after I do "Hide model-spec atoms"? Regards.

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Chains with symbol ID such as % and $ cause errors
by Ahmad Khalifa 08 Jan '20

08 Jan '20

I can do "show #2/m cartoons" for a chain with ID m, but for a chain with ID % or $, I get: show #2/% cartoons Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword

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Copy/combine function in ChimeraX
by Ahmad Khalifa 07 Jan '20

07 Jan '20

How do I duplicate (back up) a model that I already have open in ChimeraX? Regards.

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ksdssp equivalent in Chimerax
by Elliott, Jabari 07 Jan '20

07 Jan '20

Dear users, I was wondering if there was a way to adjust the preset thresholds for betasheet and helix depictions in chimerax. Essentially, I am looking for a “ksdssp” command equivalent. - “Ksdssp –s 2” Best, Jabari

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