March 2026 - ChimeraX-users - RBVI Mailing Lists

Question Regarding AI Usage in ChimeraX
by Ella Wenøe 18 Mar '26

18 Mar '26

Dear ChimeraX Support Team, I am currently working on a school research project in which I use ChimeraX to visualize and edit protein structures downloaded from the Protein Data Bank. Before I proceed, I would like to clarify one technical point: Does ChimeraX use any form of artificial intelligence or machine‑learning algorithms when loading, displaying, or editing PDB structures? In my project, I have only uploaded an existing PDB structure and made simple visual edits (such as coloring, hiding domains, etc.). I have not used any extensions, plugins, or prediction tools. However, my school requires that no AI‑based software is used unless explicitly stated, so I want to ensure that ChimeraX’s core functions do not rely on AI. Any clarification you can provide would be greatly appreciated. Thank you very much for your time. Kind regards, Ella Sophie Wenøe

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Interface between A and B chain in 4WW1.pdb
by Rosaleen Calvert 18 Mar '26

18 Mar '26

Hi Chimerax interfaces select<help:user/commands/interfaces.html#select> #1/A contacting #1/B [bothSides true][probeRadius 1.4][area Cutoff 3500] Expected a keyword What keyword is required? Have I supplied enough info? Kind Regards Rosy Calvert

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[Feature help] tile view with angular distribution
by Nguyen, Adam 16 Mar '26

16 Mar '26

Hello ChimeraX developers and users, I am looking for a feature of variant of the tile command. I have the following below with two maps each with their own angular distribution file (.BILD) which is an output from cryoSPARC to give the RELION style of angular distribution. Currently I have opened all 4 items at once and simply use the right mouse tool to translate the map and its respective angular distribution to the right. But upon rotating views, some rotation directions are not kept in place. If I were to use the tile command, it would place the angular distribution as its own item (in the case of using no flags for “tile” all four items would be in a 2x2 orientation. I am wondering if there is a way to have something similar to the tile command where you can rotate each item on its own independent axis but with multiple models/items on the same axis. For example here, I want to assess how the angular distribution of the two maps are after heterogenous refinement sorting. I want to tile the two maps and its respective angular distribution and be able to rotate them independently of the other set. [image.png] Thank you, Adam Nguyen University of Washington

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Re: [Chimera-users] Question about AlphaFold prediction in ChimeraX
by Elaine Meng 16 Mar '26

16 Mar '26

Dear Ehsan, Next time you may want to use the address for ChimeraX, chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here, since you're using ChimeraX (not Chimera). You do not need to send this question, again, however, as I already CC'd that list. You may not be doing anything wrong -- it means that AlphaFold simply didn't predict the same thing as that paper. AlphaFold and other prediction methods are not 100% accurate, and remember also that proteins may exist in multiple conformations under different conditions, etc. Of course there are different AlphaFold settings you can try, but there is no magic recipe guaranteed to give you the best result in all situations. See the AlphaFold Options help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict> 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 Mar 16, 2026, at 8:08 AM, Ehsaneh Khodadadi via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear ChimeraX Team > I am working on protein structure prediction using AlphaFold tools in ChimeraX (version 1.9 even 1.11). I am trying to model the interaction between two proteins (Tau and NDUFS3), but the predicted interaction does not match what was reported in the paper. > I followed the same steps using AlphaFold in ChimeraX (tool--->structure Prediction--->AlphaFold) and past two sequences like (sequence tau, sequence NDUFS3) and then click predict, but I could not reproduce the same beta-sheet interaction. > Could you please advise if there are specific settings or steps that might affect the prediction results? > Thank you very much for your help. > Best regards, > Ehsan Khodadadi > > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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Tools for clustering conformational ensembles?
by Oliver Clarke 13 Mar '26

13 Mar '26

Hi, Are there any tools in ChimeraX suitable for clustering/analyzing conformational ensembles, e.g. as generated by AFSAMPLE2 (https://www.nature.com/articles/s42003-025-07791-9) or similar approaches? The closest I could find was this: https://www.rbvi.ucsf.edu/chimerax/data/simstruct-doc-oct2024/simstruct.html The similarstructures interface looks great, but it seems like this can only analyze sets of structures generated in the tool - is there any way to use it to analyze an arbitrary set of structures? Basically I would like a way to (for a set of say 200 input structures of the same sequence) quickly align them and then cluster them, to identify and group representative conformational states in the ensemble of predictions. Cheers Oli

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An error opening chimerax seesion
by Yehuda Halfon 11 Mar '26

11 Mar '26

Hi all, I'm using chimeraX 0.8 (2018-12-17) on centos 7 (can't remember the build). Sometimes when I load a session that was saved using this version of chimeraX it gives me this error: Unable to restore session, resetting. Traceback (most recent call last): File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/core/ session.py", line 593, in restore obj = sm.restore_snapshot(self, data) File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/ std_commands/view.py", line 214, in restore_snapshot for k,v in data ['view attrs'].items(): TypeError: 'NoneType' object is not subscriptable After that I can't open the session again, so I need to remake it. Help, Yehuda Halfon

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Question about scale bar for segmented tomograms
by Choy, Jon 11 Mar '26

11 Mar '26

To whom it may concern: I hope this email finds you well! I am currently working with tomograms and had a question about scale bars and how they are determined. I've looked through the chimearx help dialog and it seems that the scale bar is default set to 100 angstroms, is this true? Does chimerax somehow know to pull from the metadata of the tomogram to determine the scale size? In my case I am working with segmented mrc files and am using the volume setting in the volume viewer to display the rudimentary 3D model. However, I am not sure how to verify that the 100 angstrom scale bar is correct? Any assistance would be greatly appreciated! Best, Jon

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MatchMaps difference map appears split in ChimeraX
by Francisco Murphy Pérez 10 Mar '26

10 Mar '26

Hi, I generated a difference map using MatchMaps ( https://github.com/rs-station/matchmaps) However, when I load the map in ChimeraX, the density appears split into two distinct regions. Interestingly, this does not occur when the same map is opened in Coot, where it displays as expected. I have attached a screenshot for reference. Any ideas on how to “unsplit” the map or what might be causing this behavior? Thanks in advance.

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cxc residue coloring?
by Francisco Murphy Pérez 10 Mar '26

10 Mar '26

Hi Got this cxc script (basically from copy/pasting from the log) ``` open a.pdb open b.pdb open a.mtz structureModel #1 open b.mtz structureModel #2 mm #2.2 to #1.2 bring #2.1,3 show true color byattribute r:seq_rmsd #2.2 target scab palette 0.0237942,#0fc7cf:0.258516,white:0.493237,#9e205e key cyan-white-maroon :0.024 :0.259 :0.493 showTool false select #2.2::seq_rmsd>=0.2 & ::seq_rmsd<=0.5 ``` Everything seems to work, except for the coloring. Am I missing something? Thanks

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clip
by Timothy Springer 10 Mar '26

10 Mar '26

Can you translate this into a clip command I can use in a .cxc file? clip list Using 2 clip planes: near offset -3.0783, axis -0.462,-0.880,0.109, point on plane 218.1,184.5,202.4) far offset 12.676, axis 0.462,0.880,-0.109, point on plane 210.8,170.6,204.1) - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

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