March 2026 - ChimeraX-users - RBVI Mailing Lists

Color PAE plot from structure
by Pim Huis in 't Veld 19 Mar '26

19 Mar '26

Dear ChimeraX team, I am colouring a PAE plot from a predicted multiprotein structure. From: https://www.cgl.ucsf.edu/chimerax/docs/user/tools/alphafold.html *Color plot from structure – color the plot to match the 3D structure where the pair of entities represented by an X,Y point have the same ribbon color; show the rest of the plot in shades of gray* I would like to use the correct values of the *shades of grey* to make a legend for the plot. Is there a way to see these? Is it possible to include the used palette info on the page above (as for rainbow and green)? Ideally, I would also like to change these shades of grey to have something a bit "steeper" (for example: 0 black, dark grey 5, grey 10, light grey 15, white 30). Is this already possible, or can it be added as a new palette or -ideally- as a customisable feature? Thanks a million! Pim

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Re: Easier way to reverse direction of PDB file?
by Guillaume Gaullier 18 Mar '26

18 Mar '26

Hi Mrinalini, Let's try to keep the list in CC, so the messages get archived and can help others. :-) It is difficult to understand your message without a visual. I don't know what you mean by "the stems of the proteins". But whatever it is that is going clockwise or counterclockwise, the fact that you are using these terms suggests to me that you are seeing different chiralities. I have seen it once that ab initio reconstruction followed by heterogeneous refinement produced classes of opposite chirality. This is indeed surprising, but not impossible if the starting 3D references have very low resolution (or are heavily low-pass filtered at the first iteration of the job). If you look at both maps side by side and they are mirror images of each other, then only one is a correct representation of your molecule: the one with right-handed alpha helices. (Unless you happen to work on mirror proteins made of D-amino acids, and decided to collect cryoEM data on a mixture of natural and mirror protein; but that would be a poor choice of experimental design, as it would make the image processing intractable to assign the particles to their true class.) Good luck with your project! Guillaume ________________________________ From: Mrinalini Ramanan <mrinalini.ramanan(a)gmail.com> Sent: Wednesday, March 18, 2026 5:27:46 PM To: Guillaume Gaullier Subject: Re: [chimerax-users] Easier way to reverse direction of PDB file? Dear Guillaume, Thanks for this quick yet thorough reply. Is it also possible to get maps with the wrong handedness if I have the main map going in a counterclockwise direction, and then maps from 3dva or 3d classes from this main map being in a clockwise direction? Only one of the classes is in a counterclockwise direction that matches the main map, the others are in a clockwise direction. I guess my question is regarding directionalities vs. chiral center: can two different directions result from the same chiral center? I've done vop flip on the maps and lined them up so that the stems of the proteins are aligned (with fit #1 in #2, and some with emailing), but the resulting cap directions are clockwise / counterclockwise. Thanks in advance for your help, Mrinalini Mrinalini Ramanan https://www.thehonestrational.com<https://www.thehonestrational.com/> On Wed, Mar 18, 2026, 4:54 PM Guillaume Gaullier <guillaume.gaullier(a)kemi.uu.se<mailto:guillaume.gaullier@kemi.uu.se>> wrote: Hello Mrinalini, When reconstructing a 3D volume from 2D projections in cryoEM image processing, there is a 50% probability of getting either chirality. It is relatively easy to visualize why if you cast shadows of your hands: you can easily make the shadow look the same with both your right and left hand as the object casting it, despite your two hands not being the same in 3D due to chirality. But natural proteins only have L-amino acids, their alpha helices are right-handed, etc. So the correct solution in your case is not to build a model into a map of the wrong chirality, because the only way it would work in terms of stereo-chemistry would be with D-amino acids. You simply need to mirror the map. In ChimeraX, assuming your map is loaded as model #1, this command will mirror it: volume flip #1 (The resulting mirrored map will only live in your ChimeraX session, so if you want to keep it, you need to save it as an MRC file.) There is also a job to mirror a map in CryoSPARC, if this is the program you are using to process your data: https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/util… (this is the option "flip handedness" in this job). To tell chirality only from a map, in general, you need sufficient resolution to trace the backbone, and a protein containing alpha helices: then you can determine whether they are right-handed (the correct chirality) and invert the map if they are not. Some particles have chiral features that can be identified at much lower resolution (for example the super-helical turn of DNA around nucleosomes). But it is not always easy to tell depending on particle and resolution. If auto-building programs like ModelAngelo fail or produce many short disconnected fragments when applied to a good-looking map, this is often a sign of wrong chirality. I hope this helps, Guillaume ________________________________ From: Mrinalini Ramanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: Wednesday, March 18, 2026 3:23:48 PM To: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Easier way to reverse direction of PDB file? Dear Chimerax community, I have a molecule that has a clockwise directionality for some cryoem maps, and a counter-clockwise directionality for some maps. I see this difference in directions even after fitting each map with the fit #1 in #2 command, and am now trying to build in each map. In order to create a PDB file with both directionalities, I used PyMol to do alter_state 1, obj, y = -y, rebuild, and then exported the new molecule. Is there a command in Chimera or Chimerax to do the same operations? I tried using matrix invert to no avail. Sincerely, Mrinalini VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. 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 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.

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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 11 Mar '26

11 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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