- ChimeraX-users - RBVI Mailing Lists

Guidance on SASA/RSA calculation in ChimeraX
by Kazi Sayeeda 16 Sep '25

16 Sep '25

Dear ChimeraX Support Team, I am currently using ChimeraX (v1.10.1) to study whether certain amino acid residues are surface-exposed or buried in my protein structures (WT and mutants from AlphaFold/NeuroSnap). To assess this, I measured solvent accessible surface area (SASA) with the following commands: measure sasa #1 measure sasa #1:92 measure sasa #1:562 This gives me the following SASA values (in Å²): * WT Ala92: 216.4 Å² * WT Gly562: 189.0 Å² When I compare these to published maximum ASA (MaxASA) values from Tien et al. 2013 (probe radius 1.4 Å): * Ala (max ASA) = 129 Å² * Gly (max ASA) = 104 Å² I get relative solvent accessibility (RSA) values greater than 1: * Ala92: 216.4 / 129 = 1.68 * Gly562: 189.0 / 104 = 1.82 Since RSA should not exceed 1, I believe I am mismatching ChimeraX’s calculation settings with the MaxASA reference set. So my questions are: 1. What radii model and probe radius does measure sasa in ChimeraX use by default? 2. Is there a way in ChimeraX to directly assign per-residue SASA attributes and normalize them internally (so RSA values remain ≤1)? 3. If ChimeraX defaults differ from published MaxASA tables, would you recommend reporting only SASA values, or generating my own MaxASA reference values with ChimeraX for consistency? I would be very grateful for any guidance or documentation pointers so I can report values in a way that is consistent and interpretable. Best, Kazi Sayeeda PhD Candidate Dept. of Cell and Developmental Biology (Krendel Lab) SUNY Upstate Medical University Syracuse, NY 13210 sayeedak(a)upstate.edu<mailto:%20sayeedak@upstate.edu>

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Re: scan results for vr.ucsf.edu
by Tom Goddard 16 Sep '25

16 Sep '25

Hi Greg, The web site report for vr.ucsf.edu <http://vr.ucsf.edu/> you shared takes me to web site that requires a login if I want to see what links are broken. Tom > On Sep 15, 2025, at 6:04 PM, Siteimprove Reports <reports(a)siteimprove.com> wrote: > > > Hi there, > Greg Couch (gregc(a)cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>) wants to share a dashboard report with you. The report was generated from "DCI score dashboard" at 6:02 PM on 9/15/2025. > > View report <https://reports.siteimprove.com/sendnow/8343/c77e8c4c-b3d9-4ba5-b4eb-1c17a3…> > > > > > > > > > > View report <https://reports.siteimprove.com/sendnow/8343/c77e8c4c-b3d9-4ba5-b4eb-1c17a3…> > > © 2025 Siteimprove > Havneholmen 33, DK-1561 Copenhagen, Denmark >

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Display the bfactor value when the mouse goes over a residue?
by Vincent CHAPTAL 15 Sep '25

15 Sep '25

Hello, I'd like to know, in addition to residue name and model, the bfactor of a residue when the mouse goes over it. For example model#1.20/A PHE 1482 bfactor 120.7 Could you help me to do it? Thanks a lot. 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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AlphaFold3 structures coloured in ChimeraX
by Vladimir Saudek 12 Sep '25

12 Sep '25

Hello, I am using ChimeraX 10.1 to display the results of AlphaFold3 predictions. I observe a large discrepancy between the colour coding of the quality of the structure (pIDDT) displayed at the output of the AF3 server and ChimeraX (I use the command color bfactor #1 palette AlphaFold, 1 being thenumbero of the structure to colour). ChimeraX's colouring indicates that the quality of the predicted structure is substantially lower then than that of theAF3 server. Is there any possibility to get ChimeraX to display the AF3 server colours? Below is an example, right AF3 output, left ChimedraX. Best regards Vladimir

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Determine an atom-spec from a selection
by Guillaume Gaullier 12 Sep '25

12 Sep '25

Hello chimerax-users, I am comparing different structures that all look mostly identical, and I have to generate figures of some interesting place, but they of course don't all have the same residue numbers and chain IDs (would be too easy...). I managed to work around this problem this way: - open reference structure in which I know the chain IDs and residue numbers I want to look at - open another structure, align it to the reference with mmaker - use 'select zone' with option 'residues true' and an appropriate distance cutoff from the reference structure to select the equivalent residues in the structure under scrutiny: works nicely, I simply have to tweak the distance cutoff interactively depending on how different the current structure is compared to the reference, but it is easier than looking up residue numbers and chain IDs and keeping track of all this different info per structure I am missing one thing: I would like to save these selections as named selections, so I can easily select them again further down in the script. So I need a way to say 'name someName sel' except I can't use that last 'sel' keyword because it is never expanded to the actual atom-spec that would make this trick work, and instead always points to whatever is currently selected. Is there a way to do this? I looked at 'info sel level residue' that prints to the Log something close to what I need (although more than just the atom-spec). Ideally I would like this to work from a command script, so I can automate the generation of the picture of that interesting location from many structures. Thank you in advance, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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High-Resolution images
by Khawar Siddiqui 10 Sep '25

10 Sep '25

Hi Tom, Hope you are fine. Nature Computational Science requires high-resolution VECTOR images like PDF. I noticed that ChimeraX does not have this option. Secondly, I also noticed that images can not be exported with 300-600 dpi Raster files like TIFF or PNG. How shall I proceed? I have no command-line experience. Thanking you in advance. Regards Sohail Dr Khawar Sohail Siddiqui, [cid:8e96f4e1-302e-423d-8433-4bdcdbb4da92]hoo.com This email and any files transmitted with it may contain confidential information. If you believe you have received this email or any of its contents in error, please notify me immediately by return email and destroy this email. Do not use, disseminate, forward, print or copy any contents of an email received in error.

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Re: [EXTERNAL] Question about the software features
by Elaine Meng 09 Sep '25

09 Sep '25

Hi Sepid, There is nothing to map genetic coordinates onto a structure. However, you can show the sequence that goes with your structure (if this is a protein, the amino acid sequence, NOT the DNA) in a separate window and choose residue(s) from there. How do you get the amino acid sequence? Well, you could fetch the corresponding UniProt ID, if you know what it is (e.g. go to uniprot.org <http://uniprot.org/> and search to find it), e.g. command open uniprot:LDLR_HUMAN ... or you can simply show the amino acid sequence directly taken from the structure, e.g. if it is chain B in your structure, command sequence chain /B See the Sequence Viewer documentation for how the sequence and associated structure interact. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html> I hope this helps, 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 > On Sep 9, 2025, at 3:15 PM, Mazrouee, Sepideh (NIH/OD) [E] <sepid.mazrouee(a)nih.gov> wrote: > > Hi Elaine, > > Thank you for your suggestions. While arbitrary labels could be a workaround, I need a more precise solution. > > I have a list of genetic coordinates for several protein domains generated by another program. Is there a way to map these coordinates onto the ChimeraX GUI? maybe via the “Nucleotide,” “Sequence,” or a related menu option? If I can locate the residues in the structure, I can then apply custom labels you suggested to highlight them. > > I would appreciate your help! > > Best, > Sepid

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Color cartoon transfer
by Михаил Егорочкин 07 Sep '25

07 Sep '25

Hello, my name is Michael. While using ChimeraX, I encountered a problem with transferring colored models. I created a session in Chimera where I loaded several PDB files, applied custom coloring to them, and now I want to combine the colorings from two different sessions. However, I cannot manage to do this. I tried using the .ccm format, but any session save results in a 0-byte file, and I haven’t found a solution yet. Do you have any idea how this issue can be resolved? Best regards, Michael.

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Monitor distance throughout the trajectory
by Alexandra Zahradnikova 05 Sep '25

05 Sep '25

Hi I would like to record the evolution of distance between two atoms along all points of a MD trajectory into a file but I cannot find a command to keep saving/displaying the distance in the log for the whole trajectory, just for individual points (although of course the actual distance is shown in the GUI when the trajectory is played). Thanks in advance for help. Best regards Sasha

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Re: ChimeraX bond rotation with right mouse
by Elaine Meng 05 Sep '25

05 Sep '25

Hello David Ron, For future reference, please use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here for asking questions, to ensure you get an answer. Right Mouse tool documentation says you can combine the "bond rotation" mouse mode with Shift key to move the larger side instead of the smaller side. Scroll down to see the "bond rotation" description: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> I hope this helps, 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 > On Sep 5, 2025, at 7:00 AM, David Ron <dr360(a)cam.ac.uk> wrote: > > Dear Dr. Meng, > Can you advise on a matter arising in ChimeraX [version 1.10 (2025-06-26)] > When using the right-mouse option to rotate a bond, is there an option to specify which part of the model moves and which part stays in place? > ChimeraX’s default seems set (intelligently enough) to rotate the portion of the model with the smallest mass (the fewest atoms), but sometimes it is convenient to be able to use then right mouse to rotate the bulkier part of the model, leaving the less bulky part in place. > Can this be achieved? > [I am aware of the option of using the command line to specify torsion angle about a dihedral (and which parts of the model moves), but this requires entering a specific angle of rotation and thus lacks the kind of fine control afforded by the right mouse bond rotation feature]. > Thanks for considering. > Sincerely, > David Ron > Cambridge Institute for Medical Research > University of Cambridge > Keith Peters Building > Addenbrookes Hospital > Cambridge CB2 0XY > United Kingdom > Office: +44 1223 768 940 > Mobile: +44 7941 015 666 > Email: dr360(a)cam.ac.uk

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