- ChimeraX-users - RBVI Mailing Lists

Issue with the coordset slider in chimeraX
by jeandidier.marechal＠uab.cat 05 Oct '25

05 Oct '25

Hi everyone, I am starting to take steps into ChimeraX handlers of MD simulations. So far, there have been no problems loading the starting PDB file and the trajectory. However, I am unable to make the coordset slider work. I always have the minimal version with the frame slider, the snail, and the recording button. Nothing happens when running the coordset slide #number_of_the_model. So, I can not make distance plotting and so on. I tried different versions of the software, including the latest daily build and the most recent production release. Thanks a lot for telling me what I do wrong and, if not readily implemented, please apologize for my impatience ;-) Cheers JD

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04 Oct '25

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Save centroids in scene coordinates
by Andrew Kennard 03 Oct '25

03 Oct '25

Hi there, I have aligned a bunch of models with matchmaker, and then I defined centroids for each model with `define centroid`. I would like to export those centroids for further analysis (trying to see the spatial relationship between chains B from each model when all models are aligned on chain A). However, the only way I could figure out how to do it was to press "Save Info..." in the Structure Measurements window. This text file reports the centroids in the model coordinate system for each model. But because I aligned the models with matchmaker, I'd rather have the centroids in the scene coordinate system. I am not sure how to do this transformation and export all the coordinates (~dozens of models). The only other option I found that might work was the `getcrg` command which I could use to save the coordinates to the Log, but then I will have to save the log as an HTML and parse that, right? Is there any more straightforward way? Alternatively, is there a better way to define centroids (ideally programmatically) so I can extract them from Chimera easily in scene coordinates? Perhaps the measure center command is the thing I should be using? Thanks a bunch! I'm running ChimeraX v1.10.1 (2025-07-24) on Mac OS 15.6 Sequoia Thank you!! Andrew

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de novo octahedral assembly of AlphaFold-generated ferritin monomers
by jmcquaid＠ucsd.edu 03 Oct '25

03 Oct '25

Hi folks! I would like to use "Sym # O" to model how a novel marine ferritin might assemble into an octahedral nanocage. Like ferritin, this marine ferritin is thermostable and has a size consistent with a 24-mer, but the AA sequence is too divergent to use 'matchmaker'. I've noticed that if I create a fold model of human ferritin (1FHA) with AlphaFold and import it into ChimeraX, the 'sym # O' command generates a 24-mer hairball rather than an octahedrally-coordinated sphere. If I 'fetch' the same 1FHA protein directly from PDB, the spherical structure is correctly assembled. What additional commands might be needed to help ChimeraX correctly assemble an AlphaFold-generated 1FHA monomer into the canonical ferritin cage? Chimera used to have a 'group 432' command, but I see this is not currently supported. Thanks in advance! Knowing how to correctly assemble something known like human ferritin will greatly help in assembling something unknown like a marine ferritin. Best Regards, Jeff McQuaid, Scripps Institution of Oceanography

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Re: [Chimera] local resolution map colors
by Elaine Meng 03 Oct '25

03 Oct '25

Hi, This question was sent to the commercial licensing address -- for user questions, please use the email address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here to ensure that you get an answer instead of mystified silence. Is the local resolution map open in addition to the original map? I only see two copies of the same map in the Volume Viewer. Make sure that you open the local resolution map instead of a second copy of the original map. 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 Oct 3, 2025, at 2:07 PM, Roy Chowdhury, Shatabdi wrote: > Hi, > > In the past, I've used chimerax to display local resolution on maps using the tools->volume data->surface color function. In a new map, I'm having difficulty with it. I'm attaching screenshots where the phenix local resolution job suggests the resolution range to be 1.27A - 4.6A range which is in agreement with cryosparc. When I load the cctbx_program.ccp4 file on chimerax, it is unable to color the surface and says the surface values are -0.067 - 0.107. Is there something I should be doing differently? Any suggestions would be deeply appreciated. > > Thanks! > > Shatabdi Roy-Chowdhury, PhD. > Cardiovascular Research Institute > University of California, San Francisco > > _______________________________________________ > Chimera mailing list -- chimera(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-leave(a)cgl.ucsf.edu

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Defining pdb chain ontologies
by Pranav Shah 30 Sep '25

30 Sep '25

Hi Team, I am writing to inquire about the functionality of ChimeraX, specifically concerning multi-subunit complexes with multiple chains of a single protein (e.g., PDB 4v7q). I am wondering if there is a feature that allows for manipulating chains by assigning them to functional ontologies. For instance, with the 4v7q example, I would like to be able to execute commands such as: color #1 "vp4" red `mm #1/"vp4" to #2/"vp4" These ontologies could be grabbed from the cif file and if the user decides define their pwn ontologies/groupings. If such a feature does not exist, would you consider exposing such a feature to the user? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Orient many tetramers
by Alexandra Zahradnikova 30 Sep '25

30 Sep '25

Hi I have a set of tetramers created by AlphaFold. They are randomly oriented. In order to measure their pore size in a third-party program, I need to orient them with their z axis pointing in the z direction. I can orient them with respect to the screen, but I don't know how to save this view orientation (i.e. so that the z axis in the pdb file goes vertically). Is there any way how to do it? The switch in the "save" command specifying whether to use transformed or untransformed coordinates does not make any difference, and the file is always saved in the original orientation. Best Sasha

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Suggestion for viewdock
by John Irwin 29 Sep '25

29 Sep '25

Hi Team We love viewdock. We would like to suggest allowing hotkeys for adjusting status e.g. for prioritization so that we do not need to mouse all the way down to click to change status. We think this might be a small change with a big usability and productivity impact. Thank you John John Irwin UCSF Pharmaceutical Chemistry http://irwinlab.compbio.ucsf.edu

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Just a Big Thank You
by Esmaeeli,Reza 25 Sep '25

25 Sep '25

Dear ChimeraX Developers, This is Reza and I’m a computational chemist and protein designer. I’ve been a long time user of Chimera and now ChimeraX. Among many visualization programs that I have tried extensively including PyMOL, VMD, Maestro, ChimeraX has remained my favorite. I just wanted to take a moment and write this email just to say thank you for your amazing work. Even though it is free for academic users, this email is the least I should do after so many hours that I have enjoyed using it. The interface is great. The diverse set of features and modules are awesome. And the command line and scripting capabilities are so intuitive and easy to use. Can’t wait to see what comes next. Best Regards, Reza ChimeraX 1.10.1 on macOS Tahoe

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Re: [Chimera-users] Mapping conservation onto a structure
by Elaine Meng 25 Sep '25

25 Sep '25

Hi Shelley! Chimera and ChimeraX are two separate programs, so there are various differences. The email address for ChimeraX questions, chimerax-users(a)cgl.ucsf.edu is CC'd here. I'll answer for ChimeraX since that's what you're using -- ChimeraX has a Sequence Viewer tool which is basically the logical equivalent of Chimera's Multalign Viewer, see: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html> See also the detailed tutorial on using ChimeraX to map conservation from a sequence alignment onto structures: <https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 25, 2025, at 8:36 AM, Shelley Copley via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Has Multalign viewer been taken down? I don’t see it in ChimeraX 1.10. Is there a different way to map sequence conservation onto a structure? > Thanks! > Shelley

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