- ChimeraX-users - RBVI Mailing Lists

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

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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

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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

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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.

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source code of ChimeraX
by Сергій Кущ 29 Jul '20

29 Jul '20

Hello! How to download source code of ChimeraX?

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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

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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

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Interfaces
by Reza Khayat 28 Jul '20

28 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

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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. ________________________________

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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

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