September 2025 - ChimeraX-users - RBVI Mailing Lists

About "Minimizing Structure" feature in Chimera
by Zheyun Wang (MED,124090655) 23 Sep '25

23 Sep '25

Dear ChimeraX developers: I am Wang Zheyun, a student in Chinese University of Hong Kong, Shenzhen. In my computational biology course, our professor demonstrated to us that the molecular structure (a file containing several water molecules) can be changed to an energy-minimizing structure using "Minimizing structure" function in Chimera. However, I cannot find this function in ChimeraX(1.10.1), and professor told me that these two are completely different softwares. Is this function available in ChimeraX? If so, may I know where it is? If not, will this be added to ChimeraX or is it deliberately deleted? Looking forward to your reply! Sincerely, Wang Zheyun

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Python API: locate_maximum logic
by nrajan53045＠utexas.edu 19 Sep '25

19 Sep '25

Hi there, I was hoping to implement something similar to the rigid rotation/translation optimization within fitmap due to its efficiency. I have some code which appears to implement the same logic as locate_maximum from your github, but is returning wildly different affine matrices than I expect. I just had a couple of questions regarding the logic: 1) locate_maximum receives an conversion matrix from world to voxel space (xyz to ijk) as one of its parameters from volume's matrix_and_transform function. I was wondering what this matrix actually is? I was tracing through the matrix_and_transform function and I couldn't really figure this out. I am currently assuming that the transform matrix is a 3 x 4 affine matrix: 1/v * (I | -O). Where v is the isotropic voxel size, I is a 3 x 3 identity matrix and O is a 3 x 1 vector representing the origin of the map. 2) Within each step of a segment, the following is done (from steps_to_maximum): ``` if step_types: for step in range(steps): calculate_step = step_types[step % len(step_types)] xyz_to_ijk_tf = xyz_to_ijk_transform * move_tf step_tf = calculate_step(points, point_weights, rotation_center, data_array, xyz_to_ijk_tf, ijk_step_size, metric, syminv = syminv, values = values, gradients = gradients) move_tf = move_tf * step_tf ``` In this loop, xyz_to_ijk_transform looks like the full conversion matrix from world to voxel space. But each iteration also multiplies it by move_tf before applying the step calculation, and then updates move_tf again with step_tf. At first glance, it seems like we’re reapplying the same full transform at every step... so why not just apply it once, instead of multiplying it repeatedly inside the loop? And then when we return to locate_maximum, move_tf is once again applied to the full conversion matrix. before continuing the iteration. I apologize if this is nitty gritty detail, but I would really like to make sure my logic is sound when I am implementing my version of this algorithm. Thank you for your time, Nikhil Rajan

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Generate a volume from a shape
by Guillaume Gaullier 18 Sep '25

18 Sep '25

Hello, I am trying to do something seemingly simple, but can't figure out what I am doing wrong. I have an mrc map open as model #1, moved the center of rotation somewhere, then generated a sphere with: shape sphere radius 30 center cofr I got a sphere as model #2, good. Then I want to turn this sphere into a mask, which I try doing like this: volume onemask #2 ongrid #1 At which point I get this error: Expected a density maps specifier or a keyword The documentation of 'volume onemask' says it needs a surface specification as the first argument, and the model panel shows that there is no surface associated to the sphere (then why/how is it displayed? not sure), so that all seems to make sense. And I am stuck at this step: how do I turn this sphere into a surface so I can generate a volume from it? I read the documentation for 'surface', 'volume' and 'shape' but can't find anything to solve this problem. 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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Predicting and modeling post-translationally modified C-terminal endings
by Parks, Ryssa 16 Sep '25

16 Sep '25

Hello, I am trying to predict and model a peptide docking to a receptor protein using ChimeraX's AlphaFold interface, and I was wondering if there is any way to specify post-translational modifications in the AlphaFold input function in ChimeraX? Our peptide has an amidated C-terminus, and my searches online have not yielded much success. Thank you, Ryssa Parks

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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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