- 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 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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ChimeraX Help: Selective residue labeling for peptide/Protein interface !
by Arun Gupta 09 Mar '26

09 Mar '26

Dear ChimeraX Team, I am currently working on visualizing peptide/Protein complexes and I’m having some trouble maintaining specific residue labels while clearing others. My Goal: I want to label: 1. Protein (Chain A) residues that are within 5.0Å of the Peptide (Chain C) residue 1. 2. The Peptide (Chain C) P1 residue itself. 3. I want to ensure residues P2–P9 remain unlabeled. Below is the script I am currently using: set bg white graphics silhouettes t lighting depthCue f size #1 ballScale 0.20 stickRadius 0.2 select /A & (/C:1 :<5.0) show sel style sel ball color byhet view sel label sel text "{0.label_one_letter_code}{0.number}" label @@display residues bgColor white label height 1.0 sel #1/C: 2-9 label delete The issue I am encountering is that when I execute: sel #1/C: 2-9 label delete it deletes not only the labels for peptide residues P2–P9, but also the labels for the protein interface residues that were previously defined and labeled. Question: * Should I be using a more specific selector in the label command itself to avoid using select and label delete sequentially? Any advice on the cleanest syntax to achieve this would be greatly appreciated! Best regards, Arun Arun Gupta PhD, MRSC Sr. Post Doctoral Research Assistant Gillespie/McMichael Group Nuffield Dept. of Clinical Medicine, University of Oxford, Centre for Immuno-Oncology Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ Tel: + 44 (0)1865 2612913

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Question about changes in alphafold contacts command
by Rowan Cain 09 Mar '26

09 Mar '26

Hello, I am an undergraduate doing research involving protein protein interactions in C. elegans, and I have recently been having some issues with the alphafold contacts command when measuring buried area in protein-protein interfaces. I am running the same batch of dimers that was measured a few years ago with AF2 data, and now with current AF3 data I am seeing vastly different results with the same maxPae, distance values. The main change I noticed with ChimeraX is that the argument in the alphafold contacts command has been changed from “toResidues” to “toAtoms” - is there any reason why this change took place, and would it cause the amount of interacting residues to be measured differently? Thank you, Rowan Cain

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What is the best way to visualize the impact of mutations on the interaction between two proteins?
by jar636＠pitt.edu 06 Mar '26

06 Mar '26

I am working on a project regarding evolution and want to be able to make the necessary mutations on the proteins and then be able to visually see the impact the mutation has on the interaction of the proteins. Specifically, I want to be able to use this information to create a hypothesis as to why these proteins evolved based on the change in interaction. I have tried measuring the distance between the two proteins, but I was wondering what would be the best way to see the biological relevance and overall structural impact of the mutations? Thanks!

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Isolde on ChimeraX 1.11.1 download issue
by Vorländer,Matthias Kopano 05 Mar '26

05 Mar '26

Hi guys, I am trying to install ISOLDE on ChimeraX version 1.11.1 (2026-01-23) for MacOS, but the toolshed says there is no download available for this version. If I however check the Isolde release history, I find version 1.11 <https://cxtoolshed.rbvi.ucsf.edu/download/chimeraxisolde/1.11/1357> from 9 days ago that explicitly states compatibility with ChimerX 1.11.1 on MacOS. Am I missing something or is there some bug? Thanks a lot for your help, Matthias

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What is the ChimeraX color gamut for hex codes?
by Andrew Kennard 05 Mar '26

05 Mar '26

When I color models using hex codes of colors I would like, they are noticeably brighter than the colors I am trying to specify with RGB hex codes. I am selecting colors based on the rest of my figure (which is being built in the sRGB colorspace/color gamut in Adobe Illustrator). I realize that the lighting settings in ChimeraX can change apparent colors, so I am using the "Flat" rendering mode to hopefully minimize that effect. But when I take a hex code I have selected in Illustrator and try to color the model with that hex code, the result is generally brighter than the color I specified. I suspect this is a mismatch in color gamut, but maybe it is still due to lighting? Is there a way to modulate the lighting in such a way that I can try to recover the colors I intend? Thanks! Andrew

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what information goes out from Boltz calculations
by Elaine Meng 05 Mar '26

05 Mar '26

Hi Kirk, Changing subject line and sending to the recommended address for ChimeraX questions chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (just don't include anything proprietary when using it, since it has a public archive), as I'm not the expert on this topic. Others may be able to answer your question more definitively. However, if I had to guess I would say it doesn't send ligand info anywhere because Boltz runs on your local machine, not on Colab, as per the documentation: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/boltz.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 Mar 4, 2026, at 3:22 PM, Kirk Nelson <knelson(a)tyra.bio> wrote: > > Hello Elaine, > > It is super cool that Boltz was added to ChimeraX. > > Can you please confirm whether any ligand information is queried against the external database (api.colabfold.com)? > > Thank you, > Kirk Nelson > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: Thursday, December 18, 2025 at 12:35 PM > To: chimerax-announce(a)cgl.ucsf.edu <chimerax-announce(a)cgl.ucsf.edu> > Subject: [chimerax-announce] UCSF ChimeraX 1.11 release > > =-=-=-=-=-=-= > UCSF ChimeraX version 1.11 has been released! > > This will be the last release to support Red Hat Enterprise Linux 8 and > its derivatives. > > ChimeraX includes user documentation and is free for noncommercial use. > Download for Windows, Linux, and MacOS from: > https://www.rbvi.ucsf.edu/chimerax/download.html > > Updates since version 1.10.1 (July 2024) include: > > - 2D Labels and Arrows GUI > - Boltz 2 structure prediction of proteins, nucleic acids, and > small-molecule ligands, with affinity prediction > - Boltz 2 batch ligand-binding predictions (many ligands to same receptor) > - General minimization (including ligands) with Minimize Structure tool > and "minimize" command > - new ViewDock interface (replacing previous ViewDockX) > - new types of trajectory plots: H-bonds, RMSD > - save trajectory plots to image file > - Thermal Ellipsoids GUI > - "chirality" command to report stereocenter chirality > - save/restore scenes including atomic, ribbon, and volume styles and > coloring; more to be added later > > For details, please see the ChimeraX change log: > https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog > > Enjoy! > On behalf of the team, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco

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VR on ubuntu workstation
by arangarajan＠initialtx.com 04 Mar '26

04 Mar '26

Hi, i got steam VR installed but later found out that Oculus does not support linux. Is there a work around for using chimerax VR on latest ubuntu machine with oculus rift s headset? i can get other headset also if it will fit this purpose. thanks in advance, best amith

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RSA Values on Per Residue Basis
by Haley Breckenridge 04 Mar '26

04 Mar '26

Good morning, Is there a way for ChimeraX to calculate RSA values on a per residue basis for an entire structure? I've found software online that can do it by chain, but my structure is made of multiple overlapping chains that would impact RSA values. I understand there is the Interface function in ChimeraX, but I cannot find a way for it to tell me RSA values for each residue in a structure. Thanks! Haley Breckenridge *Haley Breckenridge* PhD Student Molecular Virology Case Western Reserve University

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Import attribute?
by Alexandra Zahradnikova 02 Mar '26

02 Mar '26

Hi All, is it possible to import residue attributes from a text/csv file? For instance, I have some data calculated at an external server, and the output is per residue in CSV format. I would like to view it as color-coded molecule, using the command "render by attribute". Is it possible? Or if not, do you know some workaround? Also, I have these data in a pymol file but I don't use pymol. Is there any way how to read a pymol (CSE) file into chimeraX? Best Sasha ________________________ Alexandra Zahradnikova Institute of Experimental Endocrinology Biomedical Research Center Slovak Academy of Sciences Bratislava Slovakia

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ISOLDE and secondary structure restraints
by Guido Hansen 02 Mar '26

02 Mar '26

Hi all, I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess: Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script? Cheers, Guido -- PD Dr. Guido Hansen Group Leader UNIVERSITÄT ZU LÜBECK INSTITUT FÜR BIOCHEMIE Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen(a)biochem.uni-luebeck.de www.biochem.uni-luebeck.de [1] Ratzeburger Allee 160 23562 Lübeck Links: ------ [1] http://www.biochem.uni-luebeck.de

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Help with capping of helices - ribbon style
by Eliane Hadas Yardeni 27 Feb '26

27 Feb '26

Hello, Recently I downloaded the new version of ChimeraX and noticed that in the ribbon style the helices now look hollow. In the older version of chimera, the helices were capped. Is there a way to cap the helices in the new version? Below is an example from the old version and the new version: Old: [cid:1fff36fe-586e-4307-98f3-a2f03b125fde] New: [cid:86e871a6-1c71-4488-9bc3-f1b209a57bec] Thank you for your help. Best, Eliane

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Cannot specify chain ID using /B:300 notation in .defattr file
by Anne-Frances Miller 27 Feb '26

27 Feb '26

Dear All, I can make .defattr files that work well for render-by-attribute, if I specify residues only as :arg or :206 (examples). However if I want to specify a particular residue in a particular chain (e.g. /A:206), I can load a .defattr file with no error, but the attribute is not found by the render-by-attribute or select-by-attribute capabilities. (I did not attempt the retired :206.A notation. Maybe I should ?) Has anyone gotten chain-specific resIDs to work in a .defattr file please? Thank you •—•—•—•—•—•—•—•—•—•—•—•—• A.-F. Miller, Ph. D. (she/elle/sie) Gill Eminent Professor Distinguished Prof. of Arts and Sciences Professor of Chemistry University of Kentucky https://uky.zoom.us/j/3250841836 https://millerlablive.wordpress.com/

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Canno specify chain ID using /B:300 notation in .defattr file
by Anne-Frances Miller 27 Feb '26

27 Feb '26

Dear All, I can make .defattr files that work well for render-by-attribute, if I specify residues only as :arg or :206 (examples). However if I want to specify a particular residue in a particular chain (e.g. /A:206), I can load a .defattr file with no error, but the attribute is not found by the render-by-attribute or select-by-attribute capabilities. (I did not attempt the retired :206.A notation. Maybe I should ?) Has anyone gotten chain-specific resIDs to work in a .defattr file please? Thank you - • - • - • - • - • - • - • - • - A.-F. Miller, Ph. D. (she/elle/sie) Gill Eminent Professor Distinguished Prof. of Arts and Sciences Professor of Chemistry University of Kentucky https://uky.zoom.us/j/3250841836 https://millerlablive.wordpress.com/

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Reproducible image generation
by Guillaume Gaullier 25 Feb '26

25 Feb '26

Hello chimerax-users, I generated images using a command script, which is mostly reproducible on the same computer (so long as I don't change the size of the 3D window between runs). However, when running the script with the same map and model files but on a different computer, I get slightly different images: different dimensions, different aspect ratio. I assemble these images in multi-panel figures in Inkscape, with linked images so the panels automatically update when I regenerate the images from ChimeraX: this is very helpful to quickly iterate changes in display style, colors etc. and see how they look in the multi-panel figure. So I need reproducibility because, if the new images have different dimensions, the objects of interest in these images will move relative to the annotations around them in the multi-panel figure. Even worse, when the aspect ratio of the new image is different, Inkscape forces it into the aspect ratio of the original image that was inserted into the multi-panel figure, so the new image is squished or stretched in one direction. Obvious solution: do it all on the same computer. In this specific case I could do that (and probably will), but what if the first computer was no longer functioning? I'd like to have a solution if this ever happens, and preferably one that doesn't require me to manually fix every single one of the now misplaced vector elements (this almost amounts to making the multi-panel figure from scratch again). I tried two different things to fix this, hoping to get two different computers to produce identical images (same number of pixels in width and height, same centering of the scene), but none seemed to produce completely reproducible results: 1) I ran the "windowsize" command on computer A with the ChimeraX window as I would have it to generate the images (in this case, maximized). Then I wrote this command in the script with the values obtained on computer A, and ran this script on computer B. The image generated on computer B now has the same aspect ratio than the one generated on computer A, but still has different dimensions. I guess this is because the two screens have different pixel densities? This trick also only worked with the ChimeraX window not maximized on computer B, which could be because its screen has more pixels so needs less "screen space" to make the equivalent image size (in pixels) as the one from computer A. 2) In addition to the "windowsize" command, I specified image width and height explicitly in my save command, setting them the same as the dimensions of the image generated on computer A. This is getting closer: the image from computer B now has the same aspect ratio and same dimensions as the image from computer A. But the outlines of "graphics silhouettes true" appear thicker in the new image than in the original. Is there a fully reproducible way to generate images on different computers with different displays? Thank you, 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

4 4

Scenes as in chimera
by Rapisarda, Chiara /FR 25 Feb '26

25 Feb '26

Hello, I would like to make movies as I used to with chimera using scenes so that smooth transitions to show different things can then be tweaked to modify figures if needed. Is it possible with chimeraX? I didn’t see anything about it? I remember there was a thread about saving each scene separately which is what I do as cxs, but I have not seen anything about putting the scenes together to make a movie. Can anybody help, or could this be implemented in chimeraX if it is not available? Also another feature that I miss about chimera is the ability to select a colour palette from colorbrew. I still do that manually, but in Chimera that was a choice in the list and it makes figure making so much easier. Thank you for all the nice work on the tool anyway. Best, Chiara Chiara RAPISARDA Senior Principal Scientist I, Group Head Bio Structure and Biophysics +33 (0)1 58 93 21 95 chiara.rapisarda(a)sanofi.com<mailto:chiara.rapisarda@sanofi.com> 13 quai Jules Guesde, 94400 Vitry S/Seine, France [signature_3187861101]<https://www.sanofi.com/> [signature_825373031]<https://www.facebook.com/sanofi/> [signature_3246108776] <https://www.twitter.com/sanofi/> [signature_579974037] <https://www.linkedin.com/company/sanofi/> [signature_2146776366] <https://www.instagram.com/sanofi/> [signature_2874155821] <https://www.youtube.com/user/sanofiaventistven>

3 2

Volume eraser as cube?
by Oliver Clarke 25 Feb '26

25 Feb '26

Hi all, Hope the chimeraX team & community are having a great start to 2025! There are often situations (in single particle cryo-EM) where I would like to erase using a plane rather than a sphere - e.g., when I want to chop off density protruding from a nanodisc or micelle in order to make a mask. There are various workaround ways to do this (e.g. just making the sphere enormous, making a cubic/rectangular mask and multiplying/substracting, etc), but I was wondering if this is a common enough scenario (perhaps other users can chime in?) that it might be worth adding the option of erasing using a cube rather than a sphere? Cheers Oli

3 2

how to align models to 0,0,0 z axis for saving to PDB ?
by Mitch Murphy 24 Feb '26

24 Feb '26

please help i cant figure out how to align a complicated set of models so the barrell of my hexameric ion channel is aligned along z axis and centered at 0,0,0 to save a pdb close cd /Users/mitch/github/hmx/jahani/egfrv3 log clear # ---------------- tmCLIC1 ---------------- open ../charmmgui-clic1/step1_pdbreader.pdb id 99 center 0,0,0 color :1-23 blue color :24-58 green color :59-241 red torsion :25@c:26@n,ca,c -60; torsion :26@n,ca,c:27@n -45 torsion :26@c:27@n,ca,c -60; torsion :27@n,ca,c:28@n -45 torsion :27@c:28@n,ca,c -60; torsion :28@n,ca,c:29@n -45 torsion :28@c:29@n,ca,c -60; torsion :29@n,ca,c:30@n -45 torsion :29@c:30@n,ca,c -60; torsion :30@n,ca,c:31@n -45 torsion :30@c:31@n,ca,c -60; torsion :31@n,ca,c:32@n -45 torsion :31@c:32@n,ca,c -60; torsion :32@n,ca,c:33@n -45 torsion :32@c:33@n,ca,c -60; torsion :33@n,ca,c:34@n -45 torsion :33@c:34@n,ca,c -60; torsion :34@n,ca,c:35@n -45 torsion :34@c:35@n,ca,c -60; torsion :35@n,ca,c:36@n -45 torsion :35@c:36@n,ca,c -60; torsion :36@n,ca,c:37@n -45 torsion :36@c:37@n,ca,c -60; torsion :37@n,ca,c:38@n -45 torsion :37@c:38@n,ca,c -60; torsion :38@n,ca,c:39@n -45 torsion :38@c:39@n,ca,c -60; torsion :39@n,ca,c:40@n -45 torsion :39@c:40@n,ca,c -60; torsion :40@n,ca,c:41@n -45 torsion :40@c:41@n,ca,c -60; torsion :41@n,ca,c:42@n -45 torsion :41@c:42@n,ca,c -60; torsion :42@n,ca,c:43@n -45 torsion :42@c:43@n,ca,c -60; torsion :43@n,ca,c:44@n -45 torsion :43@c:44@n,ca,c -60; torsion :44@n,ca,c:45@n -45 torsion :44@c:45@n,ca,c -60; torsion :45@n,ca,c:46@n -45 torsion :45@c:46@n,ca,c -60; torsion :46@n,ca,c:47@n -45 torsion :46@c:47@n,ca,c -60; torsion :47@n,ca,c:48@n -45 torsion :47@c:48@n,ca,c -60; torsion :48@n,ca,c:49@n -45 torsion :48@c:49@n,ca,c -60; torsion :49@n,ca,c:50@n -45 torsion :49@c:50@n,ca,c -60; torsion :50@n,ca,c:51@n -45 torsion :50@c:51@n,ca,c -60; torsion :51@n,ca,c:52@n -45 torsion :51@c:52@n,ca,c -60; torsion :52@n,ca,c:53@n -45 torsion :52@c:53@n,ca,c -60; torsion :53@n,ca,c:54@n -45 torsion :53@c:54@n,ca,c -60; torsion :54@n,ca,c:55@n -45 torsion :54@c:55@n,ca,c -60; torsion :55@n,ca,c:56@n -45 torsion :55@c:56@n,ca,c -60; torsion :56@n,ca,c:57@n -45 torsion :56@c:57@n,ca,c -60; torsion :57@n,ca,c:58@n -45 torsion :57@c:58@n,ca,c -60; torsion :58@n,ca,c:59@n -45 torsion :22@c:23@n,ca,c 60 sym #99 C6 center :17 axis :24,58@ca newModel true setattr #1.1 chains chain_id A create true setattr #1.2 chains chain_id B create true setattr #1.3 chains chain_id C create true setattr #1.4 chains chain_id D create true setattr #1.5 chains chain_id E create true setattr #1.6 chains chain_id F create true delete #99 rename #1 tmCLIC1 rename #1.1 tmCLIC1-A rename #1.2 tmCLIC1-B rename #1.3 tmCLIC1-C rename #1.4 tmCLIC1-D rename #1.5 tmCLIC1-E rename #1.6 tmCLIC1-F # ---------------- EGFRv3 ---------------- #runscript egfrv3_v1.cxc # ---------------- OSMR ---------------- open Q99650 fromDatabase alphafold version 6 id 3.1 center 0,0,0 torsion #3.1:804@c:805@n,ca,c 60; torsion #3.1:805@n,ca,c:806@n 45 torsion #3.1:805@c:806@n,ca,c -120; torsion #3.1:806@n,ca,c:807@n 130 torsion #3.1:806@c:807@n,ca,c -120; torsion #3.1:807@n,ca,c:808@n 130 torsion #3.1:807@c:808@n,ca,c -120; torsion #3.1:808@n,ca,c:809@n 130 torsion #3.1:808@c:809@n,ca,c -120; torsion #3.1:809@n,ca,c:810@n 130 delete #3.1:836-979 rename #3 OSMR rename #3.1 OSMR-I combine #3.1 modelid 3.2 name OSMR-J setattr #3.1 chains chain_id I create true setattr #3.2 chains chain_id J create true turn x 270 models #3 turn z 180 models #3.1 move y 90 models #3 move x 200 models #3.1 move x -200 models #3.2 # ---------------- DISPLAY ---------------- delete ~protein rainbow #1-3 structures palette Paired-12 surface #1-3 transparency 0.5 move x 5.08443251 models #1 move y -47.21837099 models #1 move z -14.00102839 models #1 #turn x -67.233 models #1 center 0,0,0 #turn y -31.805 models #1 center 0,0,0 #turn z -69.036 models #1 center 0,0,0 define axis #1 primary false tertiary true radius 1 padding 100 id 4.1 define axis frompoint -300,0,0 topoint 300,0,0 color red id 4.2 define axis frompoint 0,-300,0 topoint 0,300,0 color green id 4.3 define axis frompoint 0,0,-300 topoint 0,0,300 color blue id 4.4 view position #1 sameAsModels #4.4 angle #4.1 #4.2 angle #4.1 #4.3 angle #4.1 #4.4

3 2

New ChimeraX Plugin: Cube'n Tube
by Cairoli Tamino 24 Feb '26

24 Feb '26

Hey all, I’m happy to share a small plugin I recently developed for UCSF ChimeraX: Cube’n Tube. It extends the standard eraser sphere tool. Instead of only a sphere, you can now erase with cubes, cylinders (frustum), cones, or even define your own custom shape. While working with various protein structures, I often felt that a spherical eraser is not always ideal. Especially when trying to remove part of a filament, micelle density, or isolate one asymmetric unit of a larger assembly. I was really missing a more dynamic eraser tool, so I decided to build it. I also implemented a simple undo/redo function for the eraser tool. I cannot count how often I misclicked and had to restart my masking from zero… Now there is a one-step undo (limited to one step to keep it smooth on all machines). The custom shape option works particularly well together with a fitted atomic model (for example from AlphaFold) to erase everything outside the region of interest. Cube’n Tube can be downloaded directly from the ChimeraX Tool Shed or from GitHub (https://github.com/TaminoCairoli/CubeNTube) If you are missing a feature or have ideas for improvements, feel free to open an issue on GitHub. Many thanks to the team (especially Tom Goddard) at University of California, San Francisco for building such a powerful and well-documented tool, and thanks to Pavel Afanasyev, Julius Rabl and Dianhong Wang for discussion and testing. Best, Tamino

1 0

Trouble with ISOLDE installation.
by Michel THEPAUT 23 Feb '26

23 Feb '26

Dear help team, I try to install ISOLDE from ChimeraX, using Tool / More Tools... menu: Clicking on Install looks to work, because I have the information below which appears un Log of ChimeraX But it looks like nothing happens as progression bar (red arrow above) do not progress, even after more than half an hour. I am using ChimeraX installed thanks to SBGrid: Is there a known problem or an other way to do this installation ? Thank you for your help. Best regards. -- Michel Thépaut Institut de Biologie Structurale MIT/M&P CAMPUS EPN 71 avenue des Martyrs CS 10090 38044 Grenoble Cedex 9

2 2

Improvements to ChimeraX 1.11.1
by Anindya Karmaker 20 Feb '26

20 Feb '26

Hello, I am a final year grad student at UCD and among many of my passions and recently acquired skills molecular biology/simulation is one of them. I have been using ChimeraX for some time now to learn and have used it extensively as well. But with every changing version I find wide gaps between functions.In the recent version 1.11.1 some commonly used functions like icoshedral have been completely removed and syntax changed. I develop applications for fun and utility as well and I understand that change is necessary. But you also have to understand backward compatibility. You simply cannot remove a function and expect people will adapt to it. Please do not remove syntax and backward compatibility. I understand that you may or may not be using AI to improve the application but one thing I found is that AI will hallucinate and will try to make changes or rewrite unnecessary code to prove its superiority which sometimes just removes backward compatibility. I would really appreciate it if you would understand my frustration. Just my two cents. Thank you. Sincerely, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker(a)ucdavis.edu <akarmaker(a)ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/>

4 10

Helpful cheat sheet for ChimeraX
by Alejandro Daniel Pereira 19 Feb '26

19 Feb '26

Hi ChimeraX team, My name is Alejandro Pereira, and I am a PhD candidate in the Trent Lab with the Department of Microbiology at the University of Georgia. I recently created a ChimeraX cheat sheet that highlights a range of useful features and includes publication‑quality examples. As a developing scientist, effective science communication is extremely important to me. With that in mind, I wanted to ask whether the ChimeraX team might be interested in including this cheat sheet on your documentation page or website. My goal is to provide beginners with a clear, accessible resource that introduces core concepts and showcases key features without the potential confusion of navigating extensive documentation. If this is something you’re interested in, please let me know, and I’d be happy to send it over. I only ask that proper citation be included to ensure appropriate credit. I’d also be glad to adapt the material to meet any formatting or style preferences you may have. Best, Alejandro Pereira Microbiology Department Trent Lab Ph.D. Candidate e: Alejandro.Pereira(a)uga.edu<mailto:Alejandro.pereira@uga.edu> [University of Georgia]

4 3

Reading Coarse Grained Trajectories into UCSF ChimeraX
by Wijeratne, Arambewela A 12 Feb '26

12 Feb '26

Hello, I have a quick question regarding loading of coarse-grained molecular simulation trajectories generated using the HPS force-field . I have a PSF and DCD generated out of 2 systems, one that contains only protein beads and another of both protein and DNA. I find that the protein only system is read by UCSF ChimeraX and reads both the PSF and DCD of that system, while the protein and DNA system doesn't. I get this error: IndexError: Cannot create Element with atomic number 119 File "atomic_cpp/cymol.pyx", line 967, in chimerax.atomic.cymol.Element._int_to_cpp_element See log for complete Python traceback. I do want to emphasize that since the HPS model is a single bead coarse-grained model, the actual mass of the nucleic acid beads encompass the mass of the sugar and nucleobase and might not reflect any 'elemental mass', (that is what I understood of the error anyway as there were residues which are having greater mass than recorded elements.) However, despite the protein beads also having masses of entire amino acid residues, not elements, the protein only simulation rendered fine. I was wondering whether there is a work around for this? To prevent ChimeraX from seeking element/atom and just utilizing the PSF file and then reading the DCD file as is? Thank you for your time, Best, Sunera

2 2

ArtiaX memory issue
by Bullitt, Esther 11 Feb '26

11 Feb '26

hi, I am able to open a tomogram in ChimeraX, but when I launch ArtiaX and try to open the same tomogram: 1440, 1023, 512, I get the error below. Is there somewhere I can increase the memory it is allowed to use? How much does it need? thank you for any assistance. Sincerely, Esther An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command "graphics restart" after changing the settings that caused the error. GLError( err = 1285, description = b'out of memory', baseOperation = glTexImage3D, pyArgs = ( GL_TEXTURE_3D, 0, GL_R32F, 1440, 1023, 512, 0, GL_RED, GL_FLOAT, array([[[ 1.5736278e+00, 5.7081121e-01, 6.6328174e-01, ..., -1.9499358e+00, -1.1798207e+00, -3.7762100e-01..., ), cArgs = ( GL_TEXTURE_3D, 0, GL_R32F, 1440, 1023, 512, 0, GL_RED, GL_FLOAT, array([[[ 1.5736278e+00, 5.7081121e-01, 6.6328174e-01, ..., -1.9499358e+00, -1.1798207e+00, -3.7762100e-01..., ), cArguments = ( GL_TEXTURE_3D, 0, GL_R32F, 1440, 1023, 512, 0, GL_RED, GL_FLOAT, array([[[ 1.5736278e+00, 5.7081121e-01, 6.6328174e-01, ..., -1.9499358e+00, -1.1798207e+00, -3.7762100e-01..., ) ) Traceback (most recent call last): File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84, in draw_new_frame view.draw(check_for_changes = False) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188, in draw self._draw_scene(camera, drawings) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/graphics/view.py", line 259, in _draw_scene draw_opaque(r, opaque_drawings) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1559, in draw_opaque _draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1572, in _draw_multiple d.draw(renderer, draw_pass) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 936, in draw drawing = self._update_view_axis(renderer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 662, in _update_view_axis pd = self._update_3d_texture_planes(view_dir) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 714, in _update_3d_texture_planes pd = self._texture_3d_planes() ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 724, in _texture_3d_planes pd = Texture3dPlanes(self) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 1551, in __init__ self._fill_textures() File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 1668, in _fill_textures t.reload_texture(td, now=True) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 3210, in reload_texture self.fill_opengl_texture() File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 3220, in fill_opengl_texture self.initialize_texture(size, format, iformat, tdtype, ncomp, data) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 3100, in initialize_texture GL.glTexImage3D(gl_target, 0, iformat, size[0], size[1], size[2], File "src/latebind.pyx", line 40, in OpenGL_accelerate.latebind.LateBind.__call__ File "src/wrapper.pyx", line 319, in OpenGL_accelerate.wrapper.Wrapper.__call__ File "src/wrapper.pyx", line 312, in OpenGL_accelerate.wrapper.Wrapper.__call__ File "src/errorchecker.pyx", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1285, description = b'out of memory', baseOperation = glTexImage3D, pyArgs = ( GL_TEXTURE_3D, 0, GL_R32F, 1440, 1023, 512, 0, GL_RED, GL_FLOAT, array([[[ 1.5736278e+00, 5.7081121e-01, 6.6328174e-01, ..., -1.9499358e+00, -1.1798207e+00, -3.7762100e-01..., ), cArgs = ( GL_TEXTURE_3D, 0, GL_R32F, 1440, 1023, 512, 0, GL_RED, GL_FLOAT, array([[[ 1.5736278e+00, 5.7081121e-01, 6.6328174e-01, ..., -1.9499358e+00, -1.1798207e+00, -3.7762100e-01..., ), cArguments = ( GL_TEXTURE_3D, 0, GL_R32F, 1440, 1023, 512, 0, GL_RED, GL_FLOAT, array([[[ 1.5736278e+00, 5.7081121e-01, 6.6328174e-01, ..., -1.9499358e+00, -1.1798207e+00, -3.7762100e-01..., ) )

2 7

ChimeraX dowloading problem
by JORGE Y GARAY-COLON 11 Feb '26

11 Feb '26

Greetings, I am trying to download ChimeraX in my windows laptop but an error message appears (attached below) right after accepting the terms and conditions. I am selecting the ChimeraX-1.11.1.exe version. "Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error. More information about this error may be available in the server error log."

2 1

error message running fodseek
by Miller, David M 10 Feb '26

10 Feb '26

Hi, Foldseek ran successfully with PDB but crashed in an independent comparison to AlphaFold DB (see attached). Looks like a problem with alphafold file name? Thanks for your help. Best, david David M. Miller, III, PhD Professor Cell and Developmental Biology 465 21st Avenue South PMB 407935 3120 MRB III Vanderbilt University Nashville, TN 37240-7935 (615) 343-3447 https://medschool.vanderbilt.edu/miller-lab/

2 2

(no subject)
by Timothy Springer 09 Feb '26

09 Feb '26

This works for Ca and Mg but not Mn size :CA, Mg,Mn atomRadius +0.5 - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

2 1

expression
by Timothy Springer 09 Feb '26

09 Feb '26

Hi, the sidechains of residues 35 and 80 are contained within the selection. I am trying to remove the sidechains of residues 35 and 80 when saving a new name. what is wrong with this? name frozen conVup sel &~[:35,80&sideonly] name frozen conVup sel &~:[35,80]&sideonly I subsequently found I could solve it with ~select #1:35,80&sideonly name frozen conVup sel - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

2 1

Worm representation of RMSD between two structures
by ruizarroyo＠ynamlab.org 07 Feb '26

07 Feb '26

Dear ChimeraX community, I am trying to make a figure to show the loop movement between two conformations of the same protein. For that, I would like to use a worm representation following these steps: -Trim residues so they all match in length between both models. -Matchmaker to align them -Calculate RMSD -... Next? From here, I would like to compute the RMSD value for each residue pair and use it to generate a worm representation; however, I cannot find any information about how to do this in ChimeraX. Is there any manual that I am missing? I appreciate any feedback that you may provide. Looking for your response. Best, Victor Ruiz

3 2

Scenes
by Timothy Springer 05 Feb '26

05 Feb '26

Scenes has a bug with centroids in a .cxc file. When I omit the centroids, scenes works fine. 8 hydrogen bonds found define centroid #1/A:214@CD1,CD2,CE1,CE2,CG,CZ radius 0.01 Centroid 'centroid' placed at [216.18133333 173.87416667 191.88966667] close #3.1 distance #1.3 #1/V:38@NE2 color black dashes 6 radius 0.04 Distance between a4b1_12G10_VCAMD1D3_core_122_real_space_refined_123.pdb #!1/V GLN 38 NE2 and centroid #1.3: 3.474Å define centroid #2/A:214@CD1,CD2,CE1,CE2,CG,CZ radius 0.01 Centroid 'centroid' placed at [215.46366667 173.33033333 193.372 ] show :Mg color :Ca yellow style :Ca, Mg sphere Changed 12 atom styles size :CA, Mg atomRadius +0.5 Changed 12 atom radii color :Ca yellow color :Mg gray select clear windowsize 946 1210 view matrix camera 0.61619,-0.78632,0.04465,217.04,0.17445,0.080986,-0.98133,138.47,0.76803,0.61248,0.18708,205.73 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.99998,0.0014978,0.0060567,-0.7471,-0.0012816,0.99937,-0.035532,7.7363,-0.0061061,0.035524,0.99935,-6.4316,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0 scenes save vcam_inter scenes restore vcam_inter Traceback (most recent call last): File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 816, in dropEvent _open_dropped_file(self.session, p) File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 132, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 216, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 510, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 498, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 48, in open return open_command_script(session, data, file_name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py", line 171, in open_command_script _run_commands(session, commands, directory = dirname(path), log = log) File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py", line 184, in _run_commands run(session, cmd, log=log) File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/scenes/cmd.py", line 61, in restore_scene session.scenes.restore_scene(scene_name) File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/scenes/manager.py", line 102, in restore_scene self.get_scene(scene_name).restore_scene() File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/scenes/scene.py", line 198, in restore_scene model.restore_scene(scene_data) File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 273, in restore_scene Model.restore_scene(self, scene_data['model state']) ~~~~~~~~~~^^^^^^^^^^^^^^^ KeyError: 'model state' KeyError: 'model state' File "/opt/sbgrid/i386-mac/chimerax/1.11/ ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 273, in restore_scene Model.restore_scene(self, scene_data['model state']) ~~~~~~~~~~^^^^^^^^^^^^^^^ - 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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ViewDock suggestions
by Andrii Kyrylchuk 04 Feb '26

04 Feb '26

Hi Chimera team! I’d like to raise two points about the new ViewDock window: 1. It would be great to have a count of displayed ligands shown somewhere in the window. For now there’s no easy way – I either count them manually, or export a |mol2| file and use |grep ... | wc -l|. 2. If I sort ligands by something else than Total Energy (which is how they are sorted in the |mol2| file), and then use arrow keys to navigate the list (either in the ViewDock or in the 3D window) the ligands are being shown in a chaotic order, which appears to be the original order from the |mol2| file. Is it possible to fix this behavior? Thank you for the great work! Sincerely, Andrii 

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Modifying styles
by George Tzotzos 04 Feb '26

04 Feb '26

This may be trivial but the answer eludes me. In a given example, I’ve been selecting residues, set the style and deselect. Then select the bound ligand and again set a different style for it, for example size stickRadius 0.3. Somehow, the 0.3 radius translates to previously selected ligands. Thank you

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ChimeraX version 1.11.1 crashing in ubuntu 24.04
by Antonio Vila Sanjurjo 02 Feb '26

02 Feb '26

Hello! I'm having problems installing ChimeraX version 1.11.1 in ubuntu 24.04. It crashes right after execution with the following terminal output __NV_PRIME_RENDER_OFFLOAD=1 __GLX_VENDOR_LIBRARY_NAME=nvidia chimerax --debug ... Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, psutil._psutil_linux, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, PIL._imaging, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler (total: 41) Aborted (core dumped) any ideas? best, Antón _______________________________________________________ Dr. Antón Vila-Sanjurjo Professor of Genetics phone: +34 881012267 email: anton.vila(a)udc.es Facultade de Ciencias e CICA - Centro Interdisciplinar de Química e Bioloxía UNIVERSIDADE DA CORUÑA As Carballeiras, s/n. Campus de Elviña. 15071 A Coruña, España [cid:9245848e-8b33-492c-b28b-ec67d05de404]

2 1

multiplier
by Timothy Springer 02 Feb '26

02 Feb '26

Hi, I want to do select zone and hbonds commands for about 10 objects. Is there a way to do each with a single command, similar to using mm to align multiple objects to the same target? are there do loops or foreachobject commands? hbonds #1/V restrict #1/A-B color black hbonds #2/V restrict #2/A-B color black select zone #1/V 3.6 #1/A,B residues true; name frozen inter_vcam_a4b1a sel show sel atoms select zone #1/A,B 3.6 #1/V residues true; name frozen inter_vcam_a4b1b sel show sel atoms for zones, can one get contacts on both sides in a single command? - 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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pseudobonds
by Timothy Springer 01 Feb '26

01 Feb '26

What is wrong with this second line: define centroid #1/A:214@CD1, CD2, CE1, CE2, CG, CZ radius 0.075 distance #1.3 #1/V:38@NE2 setDefaults false color black dashes 6 radius 0.04 - 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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Question about DNA representation
by Enrico Martinez 29 Jan '26

29 Jan '26

Dear ChimeraX users! I have a question regarding the representation of DNA. In my input structure, the terminal base pairs are not involved in complementary pairing. When I display the entire DNA using atom activation stubs (with nucleotides ladder showStubs true), these terminal residues appear unconnected. I've tried hiding the stubs using the same command for selected terminal residues, but it also affects the entire DNA globally rather than just the terminal residues, e.g.: nucleotides sel ladder showStubs false How could I find the stubs for the selected residues only? Many thanks in advance! Enrico

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Question about ligand protonation
by Enrico Martinez 28 Jan '26

28 Jan '26

Dear ChimeraX users! I have a question about the protonation of ligands in the complex. When I protonate only a ligand (using addh :LIG) I see in the log that it takes into account the hydrogen bonds. Does it mean that it defines the protonation state of each titratable group based on its local chemical environment of binding pocket? If so, is it possible to manually define the total charge of the ligand (and protonate it according to it)? Many thanks in advance! Enrico

2 3

Color by custom attribute
by Juan Ortiz Mateu 28 Jan '26

28 Jan '26

Dear ChimeraX team, I’ve created a .deffatr file to color residues in a chain by a custom attribute (attached). It seems that ChimeraX opens it correctly: open <help:user/commands/open.html> "/Users/ortizmateujuan/MEGA/MEGAsync/MemProtLab_UV/PROYECTOS LAB/Proyecto F1L VaccV/Alphafold/scanF1L.defattr" Summary of feedback from opening /Users/ortizmateujuan/MEGA/MEGAsync/MemProtLab_UV/PROYECTOS LAB/Proyecto F1L VaccV/Alphafold/scanF1L.defattr note Assigned attribute 'ld50' to 17 residues using match mode: 1-to-1 However, when I go to Render/Select by attribute, it does not appear on the list, and when I try with commands it says: color byattribute <help:user/commands/color.html#byattribute> ld50 palette ^rdylbu No known/registered numeric attribute ld50 Could you help me with this? Thank you very much. PS. I want to unsubscribe to this mailing list. I have tried emailing chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> many times but I keep receiving these emails. Could you do it for me please? Thanks again. ______________________ Juan Ortiz Mateu Researcher PhD Student Membrane Proteins Lab Biotecmed Institute University of Valencia Av. Vicent Andrés Estellés, 19 46100 Burjassot (Valencia) Spain research.uv.es/membrana/

2 1

Saving structures
by Timothy Springer 27 Jan '26

27 Jan '26

What am I doing wrong? save midas.pdb format pdb models #1/B:1101@MG saves the entire #1 structure rather than the single atom. I have a similar problem using combine. I issue a cd command in .cxc files. But at some point during sessions, the directory switches to my home directory. I have to frequently issue the cd command. - 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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