December 2024 - ChimeraX-users - RBVI Mailing Lists

Chimerax install error
by 王康瑞 11 Dec '24

11 Dec '24

Greetings! I'm a student from Tsinghua university, thank you for your contribution. I encountered a error when I installing ChimeraX, and I pasted it in the attach files below. I was able to launch chimerax with option"--nogui", and "--help" option seems run successfully too, but the ui didnt work. Thank you! Best wishes, Kyrie.

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Question about translating/rotating individual chains in a model
by John Watters 11 Dec '24

11 Dec '24

Hi all, I was wondering if anyone had any suggestions on how to rotate and translate a DNA-bound protein model one base pair at a time (essentially walking the protein down the double helix) so I can compare its interactions with another protein. My plan was to define a vector between the center of mass of each nucleotide pair to then move the DNA-bound protein one average pitch length using the move command and rotation using the turn command one nucleotide at a time. When I try to save these new models using "save pdf_filepath.pdb models #3 relModel #1" the DNA-bound protein is still in the original position - do I need to modify the save command or move the DNA-bound protein using different commands? Thanks for any help you can provide! Best, John

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chimeraX 1.9rc202412100000 and copy/paste from the log panel not possible
by Vincent CHAPTAL 11 Dec '24

11 Dec '24

Hi, after upgrading to 1.9rc202412100000, I can't copy/paste a command from the log panel, typically the "view matrix" for the orientation. I tried it on 1.7 and it works with the 2 chimeraX sessions working at the same time. (haven't tried it on 1.8). Is there something specific I'm missing? I'm using macOS 14.6.1 Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Z-flip option for fitmap?
by Oliver Clarke 11 Dec '24

11 Dec '24

Hi, I frequently use fitmap with global search to quickly fit an initial model to low resolution EM maps at early stages of data processing. At low resolution, it is often not immediately obvious which hand of the map is correct, so I will fit to both the original map and one that has been Z-flipped. Would it be possible to add an option to do this automatically, similar to how the "resolution" flag fits a molmap of the model at the specified resolution to the map? Cheers Oli

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display pseudobonds between atoms as solid line
by Vincent CHAPTAL 11 Dec '24

11 Dec '24

Hi, I've been playing a lot with the commands but I can't seem to get it right. I'd like to display a line between 2 atoms in a model. I tried: pbond #2.1:940@O #2.1:472@O reveal true color blue dashes 1 (and variations around it) but I got an error that pbond or pseudobond are unknown commands. I also played around with distance: distance #2.1:940@O #2.1:472@O hide #4.1 color #4 blue distance style #4 dashes 0 but the distance does not appear on my screen. Could you help me work this out? Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Connecting ChimeraX to Cytoscape via your structureVizX.zip file
by Jean-François Bureau 11 Dec '24

11 Dec '24

Hi, I already use Chimera to cytoscape and I would like to add chimeraX. I downloaded your structureViZ.zip file and open it but I did not find what to do next. Thank you for your help Regards JF Bureau Institut Pasteur Paris, France

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Mac with nogui to run batch cmd
by aponysbc＠gmail.com 10 Dec '24

10 Dec '24

Hi, I'm trying to generate images in batch with chimerax from terminal on mac m2. When I run "chimerax --nogui --exit --cmd" I get the error: raise LimitationError("Unable to save images because OpenGL rendering is not available") chimerax.core.errors.LimitationError: Unable to save images because OpenGL rendering is not available ChimeraX command "graphics driver" gives: OpenGL version: 4.1 Metal -88.1 OpenGL renderer: Apple M2 OpenGL vendor: Apple Is there any way around this? I saw another post about this from 2020 that the nogui option only works on linux with offscreen. Is there any way to save images in batch from terminal? Thanks, Aaron

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Intra-chain contacts
by Rosaleen Calvert 10 Dec '24

10 Dec '24

Hi How do I get a text file of contacts A-B (NOT A-A or B-B). I have tried Show atoms Select Contacts Chain A on left. Chain B on right Uncheck intermodel Check file. Please help. Thanks. Rosy

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Error during flipping to change the handedness of the cryo-EM map
by Shardul Dhole 10 Dec '24

10 Dec '24

Hi, I was trying to change the map's handedness while trying to fit two maps in ChimeraX. However, when I use the command vop flip #3 (3 is my model number), it gives an error: *"**Expected a density maps specifier or a keyword." * How to overcome this? Thank You. -- Regards, Shardul Dhole.

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ChimeraX 1.8 release
by Elaine Meng 10 Dec '24

10 Dec '24

UCSF ChimeraX version 1.8 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html Updates since version 1.7 (Dec 2023) include: - show worm depictions of attribute values (B-factor, conservation, etc.) using Render by Attribute tool or "cartoon byattribute" command - show attribute values with atomic radii using Render by Attribute or "size byattribute" - Select by Attribute graphical interface - Join Models generalized to any covalent bond (not just peptide) - show multiple alternate locations simultaneously with "altlocs show" - "pbond" command to create arbitrary pseudobonds - "measure contactarea" to report the area of one surface within a cutoff distance of another - Segmentations tool for interactive manual segmentation in 2D slice views, 3D (desktop), or 3D (VR) can be applied to any volume data, not just medical images; several fixes and ergonomic improvements including icons to assign/deassign mouse and VR hand-controller modes with a single click - set up and analyze batch AlphaFold predictions to search for protein-protein interactions (commands for advanced users who can run ColabFold directly on Linux) support for: - reading predicted aligned error (PAE) data from AlphaFold 3 - reading docking results from MOE - fetching atomic structures and maps from PDB-REDO - fetching/display of PDB NMR-STAR restraints For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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