- ChimeraX-users - RBVI Mailing Lists

Discrete coloring and secondary structure assignment.
by Reza Khayat 13 Aug '20

13 Aug '20

Hi, I'm trying to generate a ribbons diagram where the secondary structures are defined by user and colored by user. I'm running into a problem where half of the amino acid is assigned the secondary structure and the entire residue is assigned the color. This makes for a strange image. Attached is an image. Notice how the coloring starts before the secondary structure. Any help is appreciated.? Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Limits on movies
by mailman-bounces＠cgl.ucsf.edu 13 Aug '20

13 Aug '20

From: Maria Maldonado <mmaldo(a)ucdavis.edu <mailto:mmaldo@ucdavis.edu>> Subject: Limits on movies Date: August 9, 2020 at 7:23:21 PM PDT Hi! I have a question about movies and thought you might be able to help. Is there a limit to the length of the movies other than the limit maxframes? I’ve made scripts for movies with several steps. All the motions/commands show in the ChimeraX window while it is rendering, the script gets to the end and says “movie encoded”. However, when I open the movie file, the movie is missing several frames/steps. This happens even though I increased the limit maxframes (and my movies should be shorter than 15000 to begin with). If I split the original movie into shorter chunks that works fine, but I’ll have to edit the steps together in a different programme. I was wondering if this has to do with ChimeraX, or whether maybe it could be a computer memory issue or something else outside of the programme? It seems to be worse (ie the movie file stops earlier) for larger volumes and models than for smaller ones. Thank you very much for your help! Best, Maria

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chimerax amino acid sequence
by Peter Steinhagen 09 Aug '20

09 Aug '20

Hello, I am new to chimerax. For my protein of interest, there is no PDB available, thus, I chose a similar protein. However, the amino acid sequence is different. Is it possible to change the amino acid structure in chimerax? Will this change the 3D conformation? If this does not work what would be a good solution for my problem? Thanks, Peter

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Command line utility for .cmap
by Daniel Asarnow 06 Aug '20

06 Aug '20

Hi all, I have only been able to load volume series data using the .cmap format (using a daily from this week on OS X). Is there a command-line utility, perhaps ChimeraX itself, that can generate a .cmap file from a number .mrc volumes? It would be nice to generate these on my processing machine and then only download the .cmaps to my laptop. Best, -da

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Server maintenance
by Eric Pettersen 06 Aug '20

06 Aug '20

Hi all, The servers that usually host the Chimera web site and web services will be undergoing maintenance Monday and Tuesday of next week (August 10/11), but we have jury-rigged a temporary solution that should allow the web site and services to continue to function through the maintenance window. Nonetheless, do not be shocked if the site/services wind up being down on those days. Also, mail to the Chimera mailing lists and Chimera bug reports will be not be fully processed until the servers fully come back up on Wednesday. Such mail/reports will be accepted but spooled during the maintenance window, and delivered afterward. So you probably will not get any responses until Wednesday/Thursday. --Eric Eric Pettersen UCSF Computer Graphics Lab

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ChimeraX Toolshed will be down 10-11 August 2020
by Greg Couch 05 Aug '20

05 Aug '20

Hello everyone, The ChimeraX Toolshed will be down for two days starting Monday, August 10th, 2020. This is due to a major infrastructure upgrade. We are planning to keep the regular ChimeraX web site up during that time, but there's a small chance that it will be down too. Everything should be back to normal by Wednesday, August 13th. If not, we will be frantically working on getting it back up :-). -- Greg

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Fit map in map and save result map
by Luis José Castillo Valverde 05 Aug '20

05 Aug '20

Hello, I know that the ones I am going to ask maybe a recurring question but I have not managed to solve it. I know that maps as such do not have location or rotation information, but I want to generate a new map (with a new cube I imagine) which represents the current position and rotation for a given map. I am working with "fitmap (map # 1) inmap (map # 2)" the idea is to generate the new map from the optimized map, to be able to load that new "result" map without the need to perform any other transformation. If this is possible, I wanted to know if you can give me the command list to be able to do it? I already appreciate the attention provided. Best regards, Luis -- Luis José Castillo Valverde Ingeniero en Computación, TEC Costa Rica Estudiante de maestría (MSc) académica en Computación, TEC Costa Rica Telegram: @LCastillo98 LinkedIn: luisjosecastillo98

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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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