- ChimeraX-users - RBVI Mailing Lists

Save a surface
by Zhou, Tongqing (NIH/VRC) [E] 06 Aug '25

06 Aug '25

Dear ChimeraX, Is there a way to save a surface created by the “surface” command in the PDB or cif format? Best regards, Tongqing Tongqing Zhou, Ph.D. Principal Investigator and Chief Structural Virology and Vaccinology Section Structural Biology and Structural Bioinformatics Cores Vaccine Research Center (VRC), NIAID National Institutes of Health Building T40, Room 117 (Office) Building 40, Room 4609B (Lab, shipping) Office: (301) 761-7068 Cell: (240) 695-0536 https://www.niaid.nih.gov/research/tongqing-zhou-phd tzhou(a)nih.gov<mailto:tzhou@nih.gov>

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feature request: add bring option to the align command
by Alexis Rohou 05 Aug '25

05 Aug '25

Hello, I really love (and depend on) the "bring" option to the "matchmaker" command. Occasionally though, I have to fall back on "align" when I need to specify atoms that should be superposed. Would you please consider adding a "bring" option to the "align" command? Cheers, Alexis

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ChimeraX displaying hydrophobicity
by Roy Chowdhury, Shatabdi 04 Aug '25

04 Aug '25

Hi, I'm trying to display the hydrophobic parts of a molecule, and I'm trying this command "mlp #1 map true key true palette lipophilicity range -5,5 transparency 100" When I use various values for the lipophilicity range, it does not affect the colors of the potential. They also do not have the gradients like the molecule display -> hydrophobic tab. Is there a way to make this happen? Thanks, Shatabdi Roy-Chowdhury, PhD. Postdoctoral Research Scholar, Cardiovascular Research Institute University of California, San Francisco

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Studying the structure at the positions of the mutations
by Richard melzack 04 Aug '25

04 Aug '25

Hello I have started using your excellent Chimera X 1.10.1 visualisation platform and have uploaded a protein and mutated protein onto the matchmaker screen. The RMSD is low so the general appearance is very similar. However, I was wondering (the mutated protein has a 6bp insertion and a nonsynonymous SNP) how to examine the details around the exact points of the mutations (both are on the same exon). I have tried a number of ideas. The command line doesn't like sequence or sequence #1 #2. I would be grateful for your assistance. Thank you Dr Richard Melzack

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saving submodels as separate pdbs
by Alexandra Zahradnikova 30 Jul '25

30 Jul '25

Hi All, I have a trajectory (xtc) from which I can read selected frames into ChimeraX. I can then write all frames as one pdb with many submodels. But I am not able to find out how to open the frames as separate models, or save the trajectory as separate models. I will appreciate your help. Best Sasha Zahradnikova

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ViewDock Feedback and Feature Requests
by Andrii Kyrylchuk 29 Jul '25

29 Jul '25

Hi ChimeraX team! I would like to thank you for all the magnificent work you’re doing! My work would be much harder if Chimera and ChimeraX wouldn’t exist! After testing the new ViewDock (not ViewDockX), I have a few suggestions: 1. The rating system is still a bit inconvenient to use. A quick “OK/Bad” checkmark and fixed buttons to score the current ligand (as in classic Chimera) would speed up triaging. Dragging to each cell now slows review. 2. It would be great to have a possibility to rearrange columns. Now their order seems fixed. 3. It’s impossible to select and copy text in the lower part of the window. It would be very helpful in case I want to look into a specific ligand, e.g. copy its SMILES and visualize the 2D structure. 4. The window width follows the longest data field, leaving wide blank areas (see the screenshot). Could you allow arbitrary window sizes? Thanks for considering these ideas, and for all your ongoing work on ChimeraX. Sincerely, Andrii 

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How to replace ss_id for a secondary structure region?
by Rayees Mattoo 25 Jul '25

25 Jul '25

Hi, I have a region in my structure (res 208-229) which is displayed as a discontinuous helix when I am certain it is a continuous helix. I want to modify the pdb file to consider it as a continuous helix using chimeraX. I used the following commanlines: settatr #1/K:208-229 res ss_type 1 setattr #1/K:208-229 res ss_id 999 It works. However, I believe the command assigns the same region with a new unique ss_id (999), leaving the original ss_id intact. If I want to replace the the original ss_id with a new sequence range (res 208-229) how would I do that? Also, is there a way to directly text edit pdb file secondary structure list in ChimeraX? Best Rayees

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ChimeraX color fromcartoon error
by Prafful Sharma 25 Jul '25

25 Jul '25

* Dear ChimeraX Developer, I was recently trying to color a model in chimeraX based on a similar model with the same chain IDs and residues, and so I was using the command color fromcartoon #1 target #2 as specified in the documentation however I am receiving an error that says " Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword". I assume it is asking me to add a specific color name/code, but the other models have many different colors. I tried multiple turnarounds and even took help from different AI models, but still could not solve the error. I therefore think the functionality is not active, or there is some issue with I am not able to figure out. Can you please let me know if this functionality is working, or if there is any other way I can do this? Thank you for ChimeraX and your kind help! Prafful Sharma Ph.D candidate, TH lab | Structure, function, and regulation of protein synthesis Dept. of Developmental Biology and Genetics, Indian Institute of Science, Bangalore 560012

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Obtaining a list of residues that are solvent-accessible
by Gracia Mazuca, Luis Antonio 24 Jul '25

24 Jul '25

Hello, I am currently employing ChimeraX to study features of a molecule. I am studying ribosomal RNA (rRNA) in the E. coli ribosome using the PDB model 4YBB. We are interested in seeing what residues from the 23S rRNA are solvent-accessible using a probe radius of 3Å. We are wondering if you could give us some advice on how to achieve this. We have tried a few methods we have found online, but they all yield different results. I look forward to hearing from you. Thank you very much in advance. Best, [cid:25bde0d5-3803-4708-9790-94c965927e2c] Luis Antonio Gracia Mazuca Ph.D. Research Associate Department of Chemistry and Biochemistry The University of Texas at El Paso 500 W. University Ave. El Paso, TX 79968 Office: CCSB G.0512A utep.edu<http://utep.edu/>

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issue with ChimeraX 1.10 in snapdragon windows 11
by Erramilli, Satchal 24 Jul '25

24 Jul '25

Hello, I am reaching out to ask if there are any compatibility issues with ChimeraX 1.10 in Snapdragon Windows 11. The earlier version, 1.9, worked, but 1.10 doesn't. Is this a known issue with the Snapdragon architecture? Thanks, Satchal Erramilli ============================================================ This electronic message transmission and any attachments are confidential and/or proprietary and may constitute legally privileged information of Meso Scale Diagnostics, LLC. The information is intended for solely the use of "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu>. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or the taking of any action in reliance of this information is strictly prohibited. You are not authorized to retain it in any form nor to re-transmit it, and you should destroy this email immediately. If you have received this electronic transmission in error, please notify us by telephone (240-314-2600) or by electronic mail to the sender of this email, "Erramilli, Satchal" <SErramilli(a)meso-scale.com>, immediately. ===========================================================

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