- ChimeraX-users - RBVI Mailing Lists

Orbital Viewer - Gaussian formatted checkpoint
by Matthias Bremer 08 Apr '26

08 Apr '26

Dear All, when trying to render molecular orbitals from a Gaussian .fchk file, I get the following error message: WARNING AaronTools.fileIO.FileReader.read_fchk could not create Orbitals, try increasing the max. array size to read from FCHK files I used the 6-31+G(d) basis. How can I fix this? Best regards Matthias Bremer

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vseries movie recording with frame labels
by Rayees Mattoo 06 Apr '26

06 Apr '26

Hi, I want to record a vseries movie, a total of 20 frames (frame 0-19). I used the below script. I want to include a frame label (Frame 0 to 19) as the movie oscillates across frames. The frame numbers should appear in sync with the movie frames. How can I include that and record with vseries? movie record; vseries play #1 direction oscillate loop true; wait 200; movie encode ~/Desktop/vseries_movie1.mp4 Best Rayees

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Re: [Chimera-users] Built-in residue specific annotations in mmCIF?
by Oliver Clarke 06 Apr '26

06 Apr '26

Hi all, Bringing back a long-forgotten thread from the dead... Would it be possible to incorporate self-contained annotations into mmCIF in ChimeraX (reading/writing)? I recently added a primitive little widget to do this in coot1-trimmings: https://bsky.app/profile/olibclarke.bsky.social/post/3micblpuoxc2u This adds the notes as base64 in a loop at the end, so they are persistent and can be read/written/modified by multiple users, with timestamps & 3D coordinates for each note: _cootnote_annotation_meta.version 1 _cootnote_annotation_meta.program coot-trimmings loop_ _cootnote_residue_note.id _cootnote_residue_note.auth_asym_id _cootnote_residue_note.auth_seq_id _cootnote_residue_note.pdbx_PDB_ins_code _cootnote_residue_note.label_comp_id _cootnote_residue_note.author_b64 _cootnote_residue_note.modified_utc _cootnote_residue_note.note_b64 1 A 162 ? GLY T2xp 2026-03-31T17:06:58Z dGhpcyBnbHljaW5lIGlzIHdlaXJk 2 A 196 ? GLU T2xp 2026-03-31T17:07:41Z VGhpcyBpcyBhIGdsdXRhbWF0ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUu 3 C 3006 ? K T2xp 2026-03-31T17:08:08Z VGhpcyBpcyBvbmUgb2YgdGhlIHBvdGFzc2l1bXM= The nice thing about this is it is very flexible, and it means the structure itself can contain a record of modifications, interesting sites, disease mutations, etc - and can also become a kind of "track changes" or discussion forum for the structure - facilitating conversations between collaborators, for example. If there is interest, it might be good to identify a shared format for such a loop, so notes written in Coot could be read/navigated in ChimeraX, & vice versa? Cheers Oli > On Nov 12, 2015, at 7:08 PM, Greg Couch <gregc(a)cgl.ucsf.edu> wrote: > > Noted. I've added this to the list of things to do for ChimeraX (formerly known as Chimera2). > > -- Greg > > On 11/12/2015 02:21 PM, Oliver Clarke wrote: >> Relating to this, I wonder whether it is possible to find a home for attributes calculated in Chimera 2 in one of the mmCIF fields? >> >> I mean that's the advantage of mmCIF in theory right, that it is extensible and can support attributes beyond just position and B-factor? >> >> This would make transferring custom defined or calculated attributes between different chimera sessions much easier I think, if they were inherent to the file containing the coordinates, and again would at least allow for the possibility of data exchange with other programs. >> >> Oliver. >> >> On Thu, Nov 12, 2015 at 4:49 PM, Oliver Clarke <olibclarke(a)gmail.com <mailto:olibclarke@gmail.com>> wrote: >>> I see what you mean Greg... it is not at all clear how to use this now that I look at it in more detail. >>> >>> A hack using this entry as a handle for persistent notes would certainly be useful in the medium term, but in the longer term it would be nice to have a established syntax, so that notes written in Chimera could be read and displayed in Coot, for example (see here for discussion: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=coot;8213db52.1511) >>> >>> But I guess this might require some discussion with the PDB - according to their FAQ old-school PDB files will become obsolete next year and mmCIF/PDBx will be the only game in town... >>> >>> Cheers, >>> Oliver. >>> >>> On Thu, Nov 12, 2015 at 4:22 PM, Greg Couch < <mailto:gregc@cgl.ucsf.edu>gregc(a)cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>> wrote: >>>> That is an excellent suggestion. Currently the mmCIF files from the PDB provide the free-form text for the footnote, but do not provide the data that is supposed to be in the associated conformer_family_coord_set category. And without that data, it will be difficult to figure out and show exactly which atoms/residues are associated with the footnote. It looks like that part of the mmCIF specification is unused because it is not well thought out. The conformer_family_coord_set data category makes references to CIF save frames, but currently " mmCIF does not support references to save frames or the use of save frames for purposes other than for encapsulating dictionary definitions" [ <http://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html>http://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html] And since there are no examples, so it is unclear how the mmCIF committee was expecting this to work. >>>> >>>> So until atom_sites_footnote's are "fixed", is getting access to the text okay? We could probably extract the relevant residues from the free-form text most of the time, but it would be a hack. >>>> >>>> -- Greg >>>> >>>> >>>> On 11/11/2015 10:11 AM, Oliver Clarke wrote: >>>>> Hi all, >>>>> >>>>> As discussed on the ccp4bb ( <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511>https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511) the mmCIF format incorporates an atom_sites_foornote record ( <http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_site…>http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_site…) which allows for the direct association of specific comments/annotations with particular atoms/residues. >>>>> >>>>> As part of expanding mmCIF support in Chimera2, would it be possible to consider incorporating the capacity to read, write, and display these records as labels or notes? This could be a great way of incorporating built-in-annotations in a structure pertaining to specific features that could potentially be readable by other software such as Coot and pymol. >>>>> >>>>> Cheers, >>>>> Oliver. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Chimera-users mailing list >>>>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >

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Visualizing contact sites on structures larger than atoms
by Wilson, Melissa (NIH/NINDS) [F] 03 Apr '26

03 Apr '26

Hello, I am currently using ChimeraX to reconstruct mitochondria undergoing autophagy. I am interested in visualizing contact sites between the mitolysosome, surrounding mitochondria, and endoplasmic reticulum. The clashes/contacts command<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clashes.html#options> is all in the context of atoms. Can this command be used for the purpose of larger structures? Or is there another method in ChimeraX to achieve such a visualization? All of my models are surfaces. Best, Melissa Wilson

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Issue with SVG export in CircosContacts plugin: Interface residues missing !
by Arun Gupta 03 Apr '26

03 Apr '26

Dear ChimeraX Team, Today I tested the CircosContacts plugin in ChimeraX to generate Circos plots for the peptide–MHC interface. The plugin works as expected in the CircosContacts HTML webpage, where I can see the interface residue/atom contact details between the peptide (Chain Id - C) and MHC chain (Chain Id- A). However, I am not able to observe the interface residues in the exported contacts_circos.svg file. The SVG export appears to be missing the interface residue annotations that are visible in the HTML view. I have attached the exported contacts_circos.svg file for reference. For reproducibility, I used the following command: circoscontacts #1/A restrict #1/C outputDir /Users/arungupta/010426_contacts_1 interModel true intramol false Could you please let me know whether this is expected behavior, or if there is a workaround to ensure that the interface residues are included in the exported SVG file as well or if this is a known limitation of the current version of the plugin ? Thank you for your time and for developing such a useful plugin. 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

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OpenFold Tool Model Selection Question
by Eidman, Zachary M 02 Apr '26

02 Apr '26

Hello, I’ve recently started using the OpenFold tool in ChimeraX and I’ve found it really useful so far. I’m trying to model multimeric complexes and I’m wondering if the tool automatically detects multimeric inputs and uses OpenFold Multimer as the model? I noticed in some config files there is code that detects monomeric versus multimeric input, but I don’t see any indication of what model is used in any of my output files. Any input would be greatly appreciated. Thanks! Zach Eidman

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Boltz Error in ChimeraX on Ubuntu 24 LTS (GPU Workstation)
by Neha Gandhi 02 Apr '26

02 Apr '26

Dear Team, I hope you are doing well. I am writing to report an issue with running Boltz within ChimeraX on my Ubuntu 24 LTS GPU workstation. Until yesterday, Boltz was functioning correctly and I was able to successfully predict protein–ligand binding affinities. However, starting today, the workflow has begun failing with an error (line 125) during execution. I have tried the following troubleshooting steps: - Reinstalled ChimeraX and tested both the daily build and version 1.12 - Verified GPU functionality (other tools such as OpenFold are running without issues) Current behavior: - Boltz successfully predicts ligand-only structures - Boltz successfully predicts protein-only structures - However, it fails when attempting protein–ligand complex predictions. I tried using command line but didn't work. This suggests the issue may be specific to the combined workflow rather than general installation or GPU configuration. Could you please advise on: 1. Possible causes for this error (especially related to recent updates or dependencies)? 2. Any logs or debug steps I should provide? 3. Recommended fixes or configuration changes? I would be happy to share error logs or system details if needed. Thank you for your support. Best regards, Neha Gandhi Get Outlook for Android<https://aka.ms/AAb9ysg>

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addh to only parts of a model?
by Alexis Rohou 01 Apr '26

01 Apr '26

Hi all, As specified in the documentation, in command addh, "Hydrogens are added to entire atomic model(s) even if only parts of models are specified." Given how specifically this is stated, I'm guessing there was a good rationale for doing it this way. However I am facing a situation where I'd really, really like to add hydrogens only to waters (which were added by Servalcat). For reasons that I haven't got to the bottom of, addh adds hydrogens in the wrong places in a ligand I'm working on (a peptide with a mixture of natural and non-canonical amino acids, though I'm almost certain I've observed this behavior with other, less exotic, ligands). So: what is/was the rationale for not allowing users to add hydrogens to only parts of a model? How would the developers feel about a pull request adding an option to override this behavior and only add hydrogens to the spec supplied by the user? Cheers, Alexis

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Question about multiple sequence alignment after structural superimposition in ChimeraX
by OLIVA MIGUEL, BALDOMERO 31 Mar '26

31 Mar '26

Dear ChimeraX Team and Community, First, I would like to apologize if my question is redundant. I have only recently joined the community and may have missed previous discussions on this topic. I have been a user of Chimera on macOS, but with the most recent macOS updates, I have encountered compatibility issues that have led me to transition to ChimeraX. I am currently adapting to the new interface and commands, and I appreciate the many improvements it offers. However, I am missing a feature that I frequently used in Chimera: the ability to obtain a multiple sequence alignment after superimposing several structures using MatchMaker. This functionality was very useful in my workflow. I would like to ask whether there is an alternative approach in ChimeraX to achieve this, or if there are plans to include similar functionality in future updates. Thank you very much for your time and assistance. Baldo Oliva -- -- --------------------------- e-mail:baldo.oliva@ <e-mail%3Abaldo.oliva(a)gmail.com>upf.edu Baldo Oliva Miguel, PhD Structural Bioinformatics Laboratory (GRIB-IMIM) Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine (PRBB) C/ Doctor Aiguader, 80. Barcelona-08003, Catalonia, Spain (EU) Tfn: 34-933160509 Fax: 34-933160550

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Suggestion
by Samo Lešnik 30 Mar '26

30 Mar '26

Dear developers, I have a small suggestion: if the residue name is detected as HOH, TIP3, WAT, ... (whatever the list of waters are), then the bond between H2 and H1 is not drawn, as this is an artifact of the small distance. Best regards, Samo

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color the inside of ribbon helix differently
by Daniel Larsson 30 Mar '26

30 Mar '26

Hi ChimeraX team, I would like to color the inside of alpha helices in a different color from the outside, which is a standard feature in PyMOL and the original Chimera program: https://pymolwiki.org/Cartoon_highlight_color https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribinsidecolor.html But my understanding is that this is not currently possible in ChimeraX. I found some old mailing list threads on the topic and this 5-year-old open feature request ticket with priority set to low: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/1719 Based on comments from the developers, it seems as if implementing this feature is not very straight-forward with the current ribbon rendering engine. Still, I hope you will elevate the priority and put it on the road-map for future releases as it greatly improves visibility and 3D-feeling of large ribbon-style protein structures. It would add another important tool for users of your excellent software. Best regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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ChopChopMF — official user guide now available
by Lukas Bauer 30 Mar '26

30 Mar '26

Dear ChimeraX community, An official user guide for ChopChopMF is now available. ChopChopMF is a ChimeraX plugin designed to streamline protein structure analysis — providing a GUI-based workflow for mapping sequence alignments, mutations, and protein-protein interfaces directly onto 3D structures, without requiring extensive command-line expertise. The user guide covers installation, usage, and practical workflows: https://lukasinscience.github.io/ChopChopMF/ The plugin can be installed directly from the ChimeraX Toolshed: https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxchopchopmf Feedback and suggestions are very welcome. Best regards, Lukas

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Question about clipping and transparency
by John Watters 30 Mar '26

30 Mar '26

Hello All, I am experiencing an issue when I am trying to make a movie of a series of coupled atomic models and volumes overlaid on top of each other. I cannot seem to make what I believe is called the "surface cap" transparent when I have clipped into a volume and I am showing/changing the volume. When I call the transparency command in ChimeraX itself (without the script running) it works as it should and makes the surface cap transparent, but in the movie-making script it seems like the transparency command is having no effect? Do you have any suggestions on how to deal with this? Thank you! Example .cxc code block attempt clip off; clip near -24.984; transparency #1.1 90; ######################### hide #!*.*; hide #!* models; show #!1.2 models; #show volume show #!3 models; #show atomic model transparency #1.2 90;transparency #1.2.1.1 90; wait 3 hide #!*.*; hide #!* models; show #!1.3 models; show #!4 models; transparency #1.3 90;transparency #1.3.1.1 90; wait 3 ######################### Best, John

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How to generate an alignment to color by conservation
by Victor Ruiz-Arroyo 25 Mar '26

25 Mar '26

Dear ChimeraX staff, I am trying to make a representation to display the conservation using a color scale similar to this tutorial: https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-… I have downloaded ~500 target proteins using blast, downloaded the results, and aligned them in clusta omega, which gave me this file: [image: image.png] However everytime I try to open it in chimeraX I get this matrix-like window: [image: image.png] Which is different to what I would expect based on the tutorial. In fact, if I download the .ali from the tutorial, I see the correct alignment window. I have tried different alignment formats without success, and I still get the "matrix window". What software and format do you recommend using in Chimerax? Best Victor

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chimerax-trimmings update
by Oliver Clarke 25 Mar '26

25 Mar '26

Hi all, For anyone using chimerax-trimmings, I gave it a bit of an update: https://github.com/olibclarke/chimerax-trimmings/ I reorganized it and cleaned it up, added more documentation, and took advantage of the new "synopsis" option for aliases to add a help strinng for each alias, so you can access usage info from the command line (typing help or usage followed by the alias name). I also added function keys to toggle shown models on and off, and to toggle shown maps on and off, as well as function keys to cycle through lighting presets, and a function key to cycle through model display options. Hope they are useful to some folks, let me know if so! Cheers Oli

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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

2 1

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/

3 6

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

6 14

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

4 6

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

2 2

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.

2 1

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

3 4

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

4 4

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

2 2

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

2 1

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!

2 1

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

2 1

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

2 2

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

3 2

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

3 6

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

2 2

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

2 1

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

6 9

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

3 3

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/

2 2

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/

1 0

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

4 3

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 

2 2

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

2 2

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

3 3

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

2 3

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

2 4

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

3 7

morph command
by Matzov Donna 27 Jan '26

27 Jan '26

Hello, I'm trying to morph two conformations of the same protein in which one of the helices moves while it rotates. I used the following command: #morph #1,2 frames 101 wrap t method linear minHingeSpacing 20 While moving from one state to the other, the helix mentioned above is distorted (it starts and end looking good but in the middle it loses it's helical shape). Could I add/change on of the parameters to fix that? Many thanks, Donna Matzov, PhD Department of Structural Biology Weizmann Institute of Science The Shalev-Benami Lab<https://www.weizmann.ac.il/Structural_Biology/Shalev-Benami/home>

2 1

Depicting residues as spheres and adjusting sphere dimeter
by George Tzotzos 27 Jan '26

27 Jan '26

Help will be much appreciated. I’m trying to depict residues as spheres of reduced dimeter. My commands are: select <help:user/commands/select.html> :9,11,33,38,49,50,51,52,53,64,65,66,101,105 117 atoms, 114 bonds, 14 residues, 1 model selected show <help:user/commands/show.html> sel style <help:user/commands/style.html> sel ball Changed 117 atom styles style <help:user/commands/style.html> sel sphere Changed 117 atom styles size <help:user/commands/size.html> sel ballScale 0.2 Changed 1 ball scales Likewise with: setattr <help:user/commands/setattr.html> m ballScale 0.3 create true Assigning ballScale attribute to 1 item Obviously the above commands are wrong as they fail to generate the desired effect Have a good day George

2 2

Map qScore - Chimera vs. ChimeraX
by Elaine Meng 26 Jan '26

26 Jan '26

Forwarding in case someone can help with the MapQ-speciic parts of this question. Thanks Elaine > Begin forwarded message: > > Subject: [Chimera] Chimera qScore > Date: January 25, 2026 at 10:23:00 PM PST > Cc: oliver.schanz(a)boehringer-ingelheim.com > > Dear Chimera team, > We are currently aligning our in‑house cryo‑EM structure validation with community standards and encountered an issue with reproducing Q‑scores: > The wwPDB references the original Chimera/MapQ implementation, but as Chimera is being phased out in favor of ChimeraX, we can no longer reproduce the original Q‑scores in ChimeraX. > We have already evaluated available alternatives: > ChimeraX Q‑score plugin: We observe systematic differences between Q‑scores from ChimeraX and values in wwPDB/EMDB reports. The plugin author (Tristan Croll) indicated that differences likely stem from sampling not matching the original implementation and possibly slightly different averaging. The tool has also not been actively maintained for some time. > Python implementations (e.g., jamaliki/qscore and an internal prototype): These likewise yield different Q‑scores on the same model–map pairs, likely for similar reasons. > Given this, we would appreciate your guidance on two points: > Are there plans to migrate the original Chimera/MapQ Q‑score implementation into ChimeraX? > If not (or not soon), would it be possible to obtain free or reduced‑cost access to Chimera solely for the purpose of Q‑score calculations? We are otherwise fully using ChimeraX in our workflow. > Thank you very much for your feedback. > Best regards, > Oliver Schanz > > > Oliver Schanz > IT Research, Development & Medicine > > Boehringer Ingelheim GmbH > Birkendorfer Str. 65 | 88397 Biberach > > T +49 (7351) 54-7299 <tel:+49 (7351) 54-7299> > M +49 (151) 15026220 <tel:+49 (151) 15026220> > E oliver.schanz(a)boehringer-ingelheim.com <mailto:oliver.schanz@boehringer-ingelheim.com>

2 1

changing default model display type
by Pranav Shah 26 Jan '26

26 Jan '26

Hi Team, I prefer to view my models represented in the classic ribbon-style. Is there a way I can make this a default behaviour in chimerax when opening an mmcif/pdb file? 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

2 2

viewdockx
by Bäse, Nico 26 Jan '26

26 Jan '26

Dear ChimeraX developers, I would like to visualize my docking results from swissdock. But when I open viewdockx, I always get an error No suitable models found for ViewDockX. Can You help me? ___________________________________________ Kind Regards / Mit freundlichen Grüßen M.Sc. Nico Bäse Doktorand Institut für Pflanzenwissenschaften und Mikrobiologie Mikrobiologie und Biotechnologie Ohnhorststr. 18 22609 Hamburg Raum: 3.046, Otto-Warburg-Haus Tel.: <tel:+49-40-428-16-532> +49 40 428 16 521 E-Mail: <mailto:nico.baese@uni-hamburg.de> nico.baese(a)uni-hamburg.de

2 1

Filtering solvent in MD trajectories
by Enrico Martinez 23 Jan '26

23 Jan '26

Dear ChimeraX users! I am working on the visualization of an MD trajectory where some water molecules are broken due to PBC artifacts, causing oxygen and hydrogen atoms to be separated over large distances. To address this, I currently use the following workflow: 1. Remove all bonds in water molecules near the ligand. 2. Rebuild only reasonable bonds, avoiding artifactually long bonds. 3. Remove water atoms that have no bonds per frame: perframe "~bond :HOH & :LIG :<5.0; bond :HOH & :LIG :<5.0 reasonable true; hide :HOH & @@num_bonds=0 target a" interval 1 This works well to fix visualization artifacts, but the workflow is computationally heavy, as it rebuilds bonds in every frame. Is there a way to achieve the same in a single step by simply removing waters with stretched bonds? Many thanks in advance! Enrico

2 4

named selection
by Timothy Springer 23 Jan '26

23 Jan '26

I cant get my named selections to work. Here is an example. select #1/V:80@CD2 1 atom, 1 residue, 1 model selected name test sel select clear select test Nothing selected - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

4 5

ChimeraX version 1.9 has been released
by Elaine Meng 23 Jan '26

23 Jan '26

UCSF ChimeraX version 1.9 has been released! 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 1.8 (June 2024) include: - Foldseek search and analysis of large sets of similar structures - Find Cavities tool and "kvfinder" command to identify pockets and channels in macromolecules - optional residue-level summaries of H-bond and contact calculations - "mutationscores" command for analysis and plotting of results from deep mutational scanning - "surface hidefarblobs" command for colocalization analysis of light microscopy channels - raycasting option for medical images or other maps displayed as transparent volumes - selection can be expanded to all residues associated with the same column(s) in a sequence alignment - protein structure metadata can be updated with full chain sequences - missing-structure pseudobonds are labeled with the number of missing residues (default, can be turned off in preferences) For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog On behalf of the team, 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

3 4

possible bug in map segmentation?
by Alexis Rohou 22 Jan '26

22 Jan '26

Hi all, I'm seeing unexpected behavior when I do the following: - open PDB A and corresponding MRC map A (models #1 and #2) - open PDB B and corresponding MRC map B (models #3 and #4) - match #3 to #1 bring #4 - use the "Segment Map" GUI tool to perform segmentation on #4 with default parameters except "Display at most" set to 160 and "Group by selectivity" selected instead of "Group by smoothing" The unexpected behavior is that the segmentation surfaces are all offset from the map. It looks to me like the segmentation was performed on the map as though it had never been shifted/rotated by the match command. This is with ChimeraX-1.10. My apologies - I've not had time to test whether the same happens with the latest version of ChimeraX, nor to come up with an open-source, sharable example. Cheers, Alexis

2 2

ChimeraX for 3D Model of Mitochondrion
by Wilson, Melissa (NIH/NINDS) [F] 22 Jan '26

22 Jan '26

Hello, I have a stack of serial electron microscopy images in which I segmented one single mitolysosme (basically a mitochondrion being degraded) across all the images in napari. My goal now is to create a 3D reconstruction of the mitolysosome from all the stacks. Napari hasn't been working the way I'd like. I see a lot of protein structures used in your program. Can this program support visualization of larger structures -like this organelle? Sincerely, Melissa

2 1

how MatchMaker computes RMSD and alignment scores
by EMMANUEL JAIME SIBAYAN 19 Jan '26

19 Jan '26

Dear ChimeraX Team, Dear ChimeraX Team, Thank you for the documentation on the MatchMaker tool. It explains well how the tool works. I would like to ask a very simple clarification for my thesis: How are the numerical values reported by MatchMaker actually calculated? Specifically: 1. What is the mathematical formula used to compute RMSD, and which atoms are used by default? 2. How does MatchMaker convert protein sequences into numerical alignment scores? 3. Is the alignment score simply a sum of substitution matrix values, secondary-structure scores, and gap penalties, or is it weighted or normalized? I just want to clearly explain how these numbers are obtained. Thank you very much. Best regards, Emmanuel Jaime S. Sibayan -- *The information or attachment(s) in this email is(are) strictly confidential and is(are) for the intended recipient only. Any unauthorized use, dissemination, or copy of this message or the information it contains is prohibited. The recipient has the responsibility to ensure the protection of any personal data included in this e-mail and its attachment(s). If you are not the intended recipient or you receive this email by mistake, please notify the sender immediately and delete the original message and attachment(s).*

2 2

Problem in Chimerax 1.11
by Angelika Dibijo 19 Jan '26

19 Jan '26

Hi Chimerax Team, Could you please assist me in making ChimeraX 1.11 work on my machine? It was built without error from GitLab. ./ChimeraX --version UCSF ChimeraX version: 1.12.dev202601140146 (2026-01-14) © 2016-2026 Regents of the University of California. All rights reserved. My machine is: nvidia-smi +-----------------------------------------------------------------------------------------+ | NVIDIA-SMI 570.195.03 Driver Version: 570.195.03 CUDA Version: 12.8 | |-----------------------------------------+------------------------+----------------------+ | GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |=========================================+========================+======================| | 0 NVIDIA L4 On | 00000000:E5:00.0 Off | 0 | | N/A 36C P8 15W / 72W | 45MiB / 23034MiB | 0% Default | | | | N/A | +-----------------------------------------+------------------------+----------------------+ +-----------------------------------------------------------------------------------------+ | Processes: | | GPU GI CI PID Type Process name GPU Memory | | ID ID Usage | |=========================================================================================| | 0 N/A N/A 1877027 G /usr/libexec/Xorg 39MiB | +-----------------------------------------------------------------------------------------+ The window pops up, then crashes as below. $ module load virtualgl Loading virtualgl/2.5.0 Loading requirement: libjpeg-turbo/1.4.2 $ vglrun ./ChimeraX NOTE: available bundle cache has not been initialized yet WARNING: GBM is not supported with the current configuration. Fallback to Vulkan rendering in Chromium. [1896428:1897552:0115/140239.807851:ERROR:gl_surface_egl.cc(303)] No suitable EGL configs found. [1896428:1897552:0115/140239.807872:ERROR:gl_context_egl.cc(159)] Failed to get config for surface 0 [1896428:1897552:0115/140239.807885:ERROR:gl_surface_egl.cc(303)] No suitable EGL configs found. [1896428:1897552:0115/140239.807889:ERROR:gl_surface_egl.cc(1018)] No suitable EGL configs found for initialization. [1896428:1897552:0115/140239.807892:ERROR:gpu_info_collector.cc(85)] gl::GLContext::CreateOffscreenGLSurface failed [1896428:1897552:0115/140239.807895:ERROR:gpu_info_collector.cc(597)] Could not create surface for info collection. [1896428:1897552:0115/140239.808002:ERROR:gl_surface_egl.cc(303)] No suitable EGL configs found. [1896428:1897552:0115/140239.808006:ERROR:gl_surface_egl.cc(1018)] No suitable EGL configs found for initialization. [1896428:1897552:0115/140239.808062:ERROR:gl_surface_egl.cc(303)] No suitable EGL configs found. [1896428:1897552:0115/140239.808065:ERROR:gl_surface_egl.cc(1018)] No suitable EGL configs found for initialization. [1896428:1897552:0115/140239.808068:ERROR:gpu_info_collector.cc(85)] gl::GLContext::CreateOffscreenGLSurface failed [1896428:1897552:0115/140239.808070:ERROR:gpu_info_collector.cc(597)] Could not create surface for info collection. Fatal Python error: Segmentation fault Thread 0x00007f62af7fe640 (most recent call first): File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/ssl.py", line 1382 in do_handshake File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/ssl.py", line 1104 in _create File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/ssl.py", line 517 in wrap_socket File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/http/client.py", line 1475 in connect File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/http/client.py", line 996 in send File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/http/client.py", line 1058 in _send_output File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/http/client.py", line 1298 in endheaders File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/http/client.py", line 1349 in _send_request File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/http/client.py", line 1303 in request File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/urllib/request.py", line 1348 in do_open File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/urllib/request.py", line 1391 in https_open File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/urllib/request.py", line 496 in _call_chain File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/urllib/request.py", line 536 in _open File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/urllib/request.py", line 519 in open File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/urllib/request.py", line 216 in urlopen File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/site-packages/chimerax/core/toolshed/available.py", line 62 in load File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 516 in reload_available File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/threading.py", line 982 in run File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/threading.py", line 1002 in _bootstrap Thread 0x00007f6378614740 (most recent call first): File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 in <module> File "<frozen runpy>", line 88 in _run_code File "<frozen runpy>", line 198 in _run_module_as_main 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, chimerax.pdb_lib._load_libs, PIL._imaging, 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) Segmentation fault (core dumped) Thank you so much. Please let me know if you need more information. Regards, Angel -- *ANGELIKA DIBIJO* System Administrator *Monash eResearch* Monash University, Clayton Campus M: + 61 426371313 E: angelika.dibijo(a)monash.edu W: Monash-eResearch <http://www.monash.edu.au/eresearch> We acknowledge and pay respect to the Elders and Traditional Owners of the land on which our four Australian campuses stand.

2 1

Boltz and multi align structures/ligands
by George Tzotzos 18 Jan '26

18 Jan '26

I’ve used the ChimeraX Boltz interface and obtained multiple models of the same ligand bound on to the same receptor. I’d like to find residues within 5A of the ligand. Of course, I can do this one at a time. I wonder if there’s a way to automate the process. Your help is much appreciated George

2 2

extending selections
by Timothy Springer 16 Jan '26

16 Jan '26

Hi, I am trying to select multiple interactions and include them in a single named selection. Is there a better way than this? select zone #2/A 3.6 #2 residues true; name inter2A sel select zone #2/B 3.6 #2 residues true; name inter2B sel name inter2all inter2A | inter2B This does not seem to work for me and when I try to show the selection select inter2all *it says* Nothing selected I got something similar to work for hbonds hbonds #2/A restrict #2/B-G color black name hbond_inter2 hbonds #2/B restrict #2/C-G color black name hbond_inter2 hbonds #2/C restrict #2/D-G color black name hbond_inter2 hbonds #2/D restrict #2/E-G color black name hbond_inter2 hbonds #2/E restrict #2/F-G color black name hbond_inter2 hbonds #2/F restrict #2/G color black name hbond_inter2 - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

2 1

Adjusting sphere radius
by George Tzotzos 16 Jan '26

16 Jan '26

I’ve issued the following commands for my models select <help:user/commands/select.html> #2/A:120,119,41,36,37,34,49,117 72 atoms, 68 bonds, 8 residues, 1 model selected setattr <help:user/commands/setattr.html> m ballScale 0.2 create true Assigning ballScale attribute to 2 items No changes were observed on the ball scale. Is it likely that I should be trying something different to change the ball diameter? Thank you

2 2

Subtracting Two Surfaces (.cube files) for Calculating Fukui Functions
by fsl＠displ.nl 15 Jan '26

15 Jan '26

Hello all, I'm trying to calculate Fukui functions [1] using orca, I'm trying to recreate the plots mentioned in [1] as well. Briefly, I have generated two surface files f_n+1.cube and f_n.cube. I tried running in ChimeraX's console ``` open f_n+1.eldens.cube format cube open f_n.eldens.cube format cube volume subtract #1 #2 ``` But I get is a histogram on side with the level slider, and none of the levels match with the output figure on [1]. I'm not sure how to proceed ahead. Am I missing something, isn't there a surface subtract? rather than volume subtract. The files I used for the plots are in [2]. Regards hisacro. [1]: https://www.faccts.de/docs/orca/5.0/tutorials/react/FUKUI.html [2]: https://displ.nl/pb/lactone2.tar.xz

3 3

Zones help
by Timothy Springer 14 Jan '26

14 Jan '26

I am analyzing a complex made with Alphafold with 7 protein subunits and am trying to find all the interchain contacts. The zone command is useful select zone #1/A 3.6 #1 residues true, but how can I make it find all interchain contacts at once, rather than one chain at a time? What is a command to display sidechains of all residues in the zone? I really like the PAE plot that ChimeraX makes from alphafold predictions. Could I make a similar plot of the contact residues made with the zone command? - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

3 3

ChimeraX New User Inquiry on Superimposing Proteins
by Hsueh, Vincent 12 Jan '26

12 Jan '26

Good morning UCSF ChimeraX Support Team, My name is Vincent Hsueh and I'm a P1 Pharmacy Student at Champan University. I'm a new member to the lab and it seems no one, currently with the lab, has prior experience to using ChimeraX. So far, I have isolated the Human ACE hAChE (PDB: 3LII) in the .csx file attached to the email. My PI gave me the task to superimpose to proteins, Human AChE (PDB: 3LII) colored in Beige and hTg ChEL (PDB 6SCJ) colored in Gold, but I'm having issues learning how to do it on my own. I'm trying to isolate Chain #B from PDB: 3LII with PDB: 6SCJ to see which part of 6SCJ is adjacent to 3LII prior to isolating both chains. I tried reading the ChimeraX user guide, and created the attached "in-progress(super-imposed)_final.csx file, but I'm still not sure how to do it properly. So far, I've opened my isolated PDB: 3LII model in ChimeraX, opened the PDB: 6SCJ file, used the matchmaker command, highlighted the corresponding sequences in SequenceViewer, but my PI has told me that the resulting model still has minor issues. Hopefully, I can gain some guidance in this effort to learn ChimeraX on my own, for my lab, and for future lab members! Vincent Hsueh PharmD Candidate Class of 2028 Chapman University School of Pharmacy vhsueh(a)chapman.edu<mailto:catvu@chapman.edu>

2 1

Determine angle and axis while using Matchmaker
by Sen, Anindito 08 Jan '26

08 Jan '26

Dear All, I have 2 models of a protein positioned in different places in a complex macromolecular assembly. Using Matchmaker I can align the 2 models. How can I get the angles and the axis of rotation/orientation that is calculated to align the 2 models in Matchmaker. Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu<http://microscopy.tamu.edu/>

2 1

how to make a contour plot from Gaussian16 cube file
by Steven Brawer 07 Jan '26

07 Jan '26

I have used Chimerax for proteins, and it is indeed wonderful. However, now I would like to use it to view output from the Gaussian16 "computational chemistry" program, and I am at a loss. I believe the "volume" command is what I need, but I have a LOT of trouble understanding the terminology of the user documentation for the "volume" command. Perhaps someone can be very specific and guide me in the particular procedure described below (or tell me Chimerax does not do such a thing). I have a Gaussian16 cube file for electron density. (This is electron density on grid points. Chimerax can read this file.) I would like to make a contour plot - say contours in the xy plane at z = 0. I would like to specify the number of contours. I would like to know the distance (in au units) of any point on a particular contour from the origin (x=y=z=0) or even from some arbitrary point in space. I would like some sort of legend indicating the density value of each contour. How can I set this up? It would also be nice to be able to specify any plane. Thanks very much Steve

2 1

Measuring contact area in a pdb file
by Shimberg, Geoffrey (NIH/VRC) [C] 07 Jan '26

07 Jan '26

Dear ChimeraX Developers, I was wondering if you could explain to me how to measure the contact residues/area in a pdb file containing an antibody and antigen? I have been trying to do either measure buriedArea or contactArea, but I get an error. I have been using the PDB file 7Y0W as a starter structure to then use for future structures. Let me know if you need anything else. Thank you for all your help. Geoffrey Shimberg

3 6

Surface overlapping with atomic model
by naeshi9min＠postech.ac.kr 07 Jan '26

07 Jan '26

Hi, I'm Gumin Han from South Korea. Thank you for your wonderful visualization tools. This is my first time writing a question here. I want to overlap my models with surface as shown in the link (Figure panel B) https://www.nature.com/articles/s41467-024-49516-2/figures/1 Which options should I use? Thank you for reading my E-mail and best wishes for the New Year' Best regards, 2026, Jan 7th Gumin Han

3 2

Trouble installing ISOLDE in ChimeraX
by Heng Jiang 06 Jan '26

06 Jan '26

Dear ChimeraX Support Team, I hope this message finds you well. I am currently trying to install the ISOLDE plugin in UCSF ChimeraX via Tools → More Tools…, but unfortunately, the installation does not work. I have attempted multiple approaches, but the “More Tools” window does not open. Could you please advise if there is an alternative way to install ISOLDE, such as an offline installation method or by providing the necessary plugin files directly? Thank you very much for your time and assistance. I look forward to your reply. Best regards, Heng Jiang

2 2

Is toolshed down?
by jurkeviciute.gabija＠gmail.com 06 Jan '26

06 Jan '26

Hi, Apologies to bother, but I cannot seem to access toolshed to install isolde on either chimerax 1.11 or my web browser. I checked in with some colleagues and they reported the same thing. Is the site down for the toolshed by any chance? Thanks! Gabija

2 1

Video Tutorial on Protein Interaction Modeling
by David S. Fay 05 Jan '26

05 Jan '26

Hi Everyone, Despite not really being qualified, I’ve done several protein modeling workshops at universities over the past year with some positive responses. It seems to be quite useful to a good number of scientists like myself (clueless molecular/cellular biologists etc), and in particular for less experienced users. Part of my ability to pull this off at any level has been the help I’ve received from others including the wonderful staff the ChimeraX, who I give ample props to in the video. Anyway, feel free to share with students or others who might find this useful. It’s rather long (97 minutes) and I do go into a fair bit of detail about how ipTM is determined along with some of the recently developed alternative metrics for scoring protein-protein interactions. I’ve attached the link below. I also realize that this user group is very sophisticated, so feel free to comment or correct and to add to anything I may have missed or not stated properly. Thanks and happy new year, David David S. Fay Ph.D. Professor, Department of Molecular Biology Director (PD/PI), National Institutes of Health Wyoming INBRE University of Wyoming email: davidfay(a)uwyo.edu<mailto:davidfay@uwyo.edu> <https://youtu.be/u63oYfWDBoM> [maxresdefault.jpg] David's AlphaFold WorkShop 2026<https://youtu.be/u63oYfWDBoM> youtu.be<https://youtu.be/u63oYfWDBoM>

2 1

Boltz affinity prediction
by George Tzotzos 03 Jan '26

03 Jan '26

Happy New Year to all I’m unable to find out how to obtain Boltz binding affinity predictions. Probably, I’m missing out something. Any help would be most welcome. I’m attaching a screenshot for easy diagnostics. Many thanks

2 1

help for RMSD
by marian.vincenzi 23 Dec '25

23 Dec '25

Dear Chimera staff, I am a PostDock from CNR-IBB of Naples (Italy). I am contacting you on the command "match" because I would use it to evaluate rmsd between two structures. I realized (maybe I am wrong) that the value given as output rises from the overlap only on C-alpha, but I used the command "match #1@n,ca,c,o to #2:904-976@n,ca,c,o". My aim was the RMSD evaluated on all backbone atoms and not only c-alpha. Is there anyway to get RMSD value on all backbone atome and overlap the two analysed structures ? Thank you in advance. While waiting, I wish all you team Merry Christmas and Happy New year :-) Marian

2 1

New File Format for Recent ChimeraX Versions
by kkssy141＠gmail.com 22 Dec '25

22 Dec '25

Hello, I recall installing support for the XYZ file format by following the tutorial for older versions of ChimeraX, which worked as expected: https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_read_format… However, in recent ChimeraX versions (1.10 and 1.11), the same procedure no longer works. When running devel install, I encounter the below error message. I was wondering whether the documentation might need to be updated. Thanks. Best, Siyoung ``` devel install /Users/siyoungkim/Downloads/tut_read /Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: Freeware See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#licen… for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py running bdist_wheel installing to build/bdist.macosx-10.9-universal2/wheel running install running install_lib copying build/lib/chimerax/tut_read/io.py -> build/bdist.macosx-10.9-universal2/wheel/./chimerax/tut_read Traceback (most recent call last): File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/devel.py", line 180, in _run unbound_method(bb, *args, **kw) File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/bundle_builder/bundle_builder.py", line 165, in make_install _ = self.make_wheel(debug=debug) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/bundle_builder/bundle_builder.py", line 120, in make_wheel raise RuntimeError(f"Building wheel failed: {wheel}") RuntimeError: Building wheel failed: ChimeraX_TutorialReadFormat-0.1-py3-none-any.whl ```

3 2

Re: ChimeraX Boltz prediction running eternally or failing submission to MSA server
by Arthur Kaser 22 Dec '25

22 Dec '25

Same here. Boltz2 appears to stall at api.colabfold.com<http://api.colabfold.com>, regardless of size/ length of the input sequence. Nil return at this step.

2 2

Assistance with ChimeraX
by Vinita Pant 22 Dec '25

22 Dec '25

Dear ChimeraX Team, I am currently using ChimeraX 1.10.1 (2025-07-24) for preparing my protein for molecular docking, and I would like your guidance on repairing missing side chain atoms. I have explored several resources but have not yet found a solution. I appreciate any assistance you can provide to help me navigate this process effectively. Thank you for your support. *Thanks and Regards* *Vinita Pant* *Doctoral Student (SRF)* *ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal* *Mobile No.: +91 9536940943*

2 4

Installing ChimeraX bundle with none Python file
by huybk81＠gmail.com 21 Dec '25

21 Dec '25

Hi, I am making a ChimeraX bundle. I need to read a csv file as template for the bundle. However, the template file (inside src folder) was not copied or added when installed. Is there anything that I should do to get it copied?

3 2

Read CASTP pocket file
by George Tzotzos 19 Dec '25

19 Dec '25

Hi everybody, I’m following instructions in https://rbvi.github.io/chimerax-recipes/castp/castp.html open 1pn9 readcastp /Users/george/Downloads/1pn9/1pn9.poc and get Unknown command: readcastp /Users/george/Downloads/1pn9/1pn9.poc Any ideas why this is so. Many thanks George

2 1

kvFinder tool
by George Tzotzos 19 Dec '25

19 Dec '25

I’ve opened 1PN9.pdb deleted all but chain A. I used kvfinder #1 probeIn 1.4 probeOut 4.0 The largest cavity has an ID 1.1.5. How does one identify the residues that line the cavity? Thank you

2 2

Request for ChimeraX Installation Assistance
by CykaZH 19 Dec '25

19 Dec '25

Dear ChimeraX Team, I hope this message finds you well. I am writing to seek your assistance regarding the download of the latest version of ChimeraX. Currently, I am located in China, and the download speed for the software is extremely slow, even when using a VPN or an educational network. Additionally, when attempting to download via these methods, I encountered a page requiring a license, which prevented me from completing the download. To ensure a smoother and more efficient setup process, I would like to kindly ask if it would be possible for you to send the latest version of ChimeraX in .exe format as an email attachment. This would greatly help me avoid the download speed issues and the license-related obstacles I am currently facing. Thank you for your time and support. I truly appreciate your assistance and look forward to your response. Best regards, CykaZH Affiliated Hospital of Jiaxing University

2 1

ChimeraX REST remotecontrol: CORS for localhost clients?
by Boris Steipe 18 Dec '25

18 Dec '25

Dear ChimeraX team - I am writing a local, interactive tutorial (Quarto HTML) that I want drive ChimeraX via the REST remotecontrol interface. I can send commands in JavaScript, but not read responses. Quarto serves my page locally - page origin: http://localhost:5779 - ChimeraX endpoint: http://127.0.0.1:61803/run?command=... ... but if I issue in the JS console: fetch("http://127.0.0.1:61803/run?command=help") .then(r => r.text()).then(console.log).catch(console.error); I get: Console error: - CORS blocked: “No ‘Access-Control-Allow-Origin’ header is present…” - Network panel shows 200 OK, but the Fetch promise rejects with TypeError: Failed to fetch. So: Is there a supported way (or could there be) for remotecontrol rest to emit CORS headers for localhost-only clients? Something like: - Access-Control-Allow-Origin: http://localhost:5779 (or a configurable allow-list, possibly including http://127.0.0.1:*) - Access-Control-Allow-Methods: GET, POST, OPTIONS - Access-Control-Allow-Headers: Content-Type - Handling preflight OPTIONS requests (e.g. relevant for POST ) - Even an "allow only loopback origins" mode would be sufficient. Ideally, enabling CORS would be controllable at runtime from within ChimeraX (e.g., as an option to remotecontrol rest start or a subsequent ChimeraX command), so that a teaching workflow can be fully self-contained. For example, something like: • remotecontrol rest start port 61803 cors allow-origin http://localhost:* • or: remotecontrol rest cors allow-origin http://localhost:* If there’s already an option/flag for this I would be grateful for pointers. (Or perhaps I have missed a recommended pattern.) Thank you! Boris (Nb. I do understand the security implications of CORS; this use case is strictly local (loopback only), with the goal to enable processing measurements/queries in browser-based teaching material. ) -- Boris Steipe MD, PhD Professor em. Department of Biochemistry Temerty Faculty of Medicine University of Toronto

2 2

Coloring amino acid residues by type
by Elaine Meng 18 Dec '25

18 Dec '25

Hello, I may not understand your comment, but you can certainly color amino acids specified by residue type. For example, ChimeraX commands: color :asp,glu red color :lys,arg blue color :his dodger blue I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 18, 2025, at 12:13 PM, B. Sharmila Sri <e6123008(a)sriher.edu.in> wrote: > > easy to use, but coloring the aminoacid residues by code is not working properly kindly make it possible > _______________________________________________ > Chimerax-registration mailing list -- chimerax-registration(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-registration-leave(a)cgl.ucsf.edu

1 0

Regarding Internal Server Error while Downloading Chimera X
by Piyush Mohanty 16 Dec '25

16 Dec '25

Dear Administrator, I encountered an Internal Server Error while accessing the server today while downloading the candidate version of ChimeraX. The error message suggested contacting you at root@localhost. The exact error stated was : " 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." Could you please look into this issue and correct the misconfiguration at the earliest convenience? Thank you for your assistance. Best regards, Piyush Mohanty

1 0

Download UCSF ChimeraX Internal Server Error
by Mark Guthridge 16 Dec '25

16 Dec '25

Dear Sir/Madam I am getting an Internal Sever Error when trying to download ChimeraX from https://www.rbvi.ucsf.edu/chimerax/download.html The error message indicates, "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." The times of the errors occurred between 4:20pm and 4:30pm AEDT (ie. in the 10min period before I sent this email so you can check logs for my timezone). My IP is 14.2.62.78 The errors occur: * After deleting my cache * In multiple browsers (chrome, firefox, edge) * For multiple releases of ChimeraX spanning 2017-2025 * My local home network and also my phone hotspot * For both ChimeraX and Chimera * Incognito browser Could you please help? Cheers Mark Could you please help A/Professor Mark Guthridge Room L2.09.02 Centre for Cellular and Molecular Biology (CCMB) School of Life & Env. Sciences Deakin University Burwood Highway Burwood VIC 3125 +61 3 924 45796 Important Notice: The contents of this email are intended solely for the named addressee and are confidential; any unauthorised use, reproduction or storage of the contents is expressly prohibited. If you have received this email in error, please delete it and any attachments immediately and advise the sender by return email or telephone. Deakin University does not warrant that this email and any attachments are error or virus free.

2 1

Download Links for ChimeraX 1.11 broken
by Simon Michnowicz 16 Dec '25

16 Dec '25

Dear Group the download links for the latest Chimera on page https://www.rbvi.ucsf.edu/chimerax/download.html#candidate are broken, i..e the following link is broken.. <goog_247633214> https://www.rbvi.ucsf.edu/chimerax/cgi-bin/secure/chimerax-get.py?file=curr… as well as other Unix distros regards *---Simon Michnowicz * Senior Application Specialist, High-Performance Computing *Research Support Services - eSolutions* *Monash eResearch Centre* Monash University 15 Innovation Walk, Building 75, Clayton Campus Wellington Road, VIC 3800 Australia T: +61 3 9902 0794 M: +61 3 0418 302 046 E: simon.michnowicz(a)monash.edu monash.edu

2 1

"Nearby" atoms are within X angstroms of cavity points
by Berenice E Cowfer Chavez 15 Dec '25

15 Dec '25

Hello, What is the default value of "Nearby" atoms are within X angstroms of cavity points in the Find Cavities tool? I remember it used to be 5.0 A but now when I use the tool it shows 6.0 A. Sincerely, Berenice E. Cowfer Chavez, M.S. Lab Manager, Profs. Johnson and Shoulders Labs Massachusetts Institute of Technology

2 2

Adding models as a group/subgroup using Python
by huybk81＠gmail.com 15 Dec '25

15 Dec '25

I tried to read the Programming API but was unable to find out. Right now: I created surface A1,A2,B1,B2,D1,D2, etc.. I added these surfaces in a list surfs = [] surfs.append(A1) surfs.append(A2) ... surfs.append(D2) session.models.add_group(surfs, name="All surface") This make A1,A2 as models #1.1,#1.2 etc Interestingly, I cannot even find the document for add_group. I learned this from ChimeraX recipes. Anyway, I want to organize the data a bit better to have it like this #1; Surface ---> #1.1 Surf A -------> #1.1.1 A1 -------> #1.1.2 A2 ---> #1.2 Surf B -------> #1.2.1 B1 -------> #1.2.2 B1 How can we do that? Best,

2 1

Security Inquiries
by Anh-Huy Le 15 Dec '25

15 Dec '25

Hi ChimeraX folks, I know that this is mostly research software offered through educational channels, but as part of an internal security review of software we are using, I am writing you to inquire if ChimeraX already has any systems in place to report security related issues which could include any of the following: * System breaches on your end that could affect our organization (e.g.: payment information or other types of information being stolen/breached) * Uptime status of services your provide (e.g.: like this Amazon dashboard) * Systems that when queried report the latest updates to combat known security vulnerabilities. If you do not provide these services currently, do you plan on providing these services in the future? If you do not plan on providing these services in the future, would you consider offering professional services to develop these features? Thank you so much for answering ahead of time. Sincerely, Anh-Huy Phan Le, PhD (He/him) Sr. R&D Solution Architect [signature_2852565164]-- Vir Biotechnology, Inc. ale(a)vir.bio<mailto:ale@vir.bio> | Mobile: 714-269-9663 --

2 1

bug report - pip list failure
by replacement2＠gmail.com 15 Dec '25

15 Dec '25

Hi, My apologies if this is not the best place to report a bug. There appears to be an issue with `pip list`, which may be caused by a typo in `pip.py`. Please see the traceback. It'd be great if someone can verify. Thanks. Traceback (most recent call last): File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute cmd.run(cmd_text) File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/pip.py", line 71, in pip pip_cmd.appendf("list") ^^^^^^^^^^^^^^^ AttributeError: 'list' object has no attribute 'appendf' cui5

4 4

ChimeraX Boltz prediction running eternally
by Sam Allen 10 Dec '25

10 Dec '25

Hello Tom and co., I am currently trying to use ChimeraX Boltz tool to predict the structure of some small ligands onto a GPCR and my prediction running timer just never stops. I initially attempted to install and run the tool on Windows but the install failed to import the mols folder properly multiple times (uninstall and reinstalled), after manually untaring the folder in Powershell it still didn't run (Timeout while submitting to MSA server). I then decided to switch over to my mac (M1 16GB) and while the install of Boltz in ChimeraX no longer had any error and the prediction didn't error either, the timer just continued to go up (to 26000 eventually). I figured the protein was too large (471 residues, makes sense), so I tried to rerun one of your test examples (8rf4, https://www.rbvi.ucsf.edu/chimerax/data/boltz-apr2025/runtimes.html) and still no prediction output after 20 minutes. I've tried switching from default compute device to GPU or CPU and still no difference. Additionally, in activity monitor it shows ChimeraX is taking up nearly no GPU or CPU usage, so I'm confused as to what is happening. Do you have any advice or know anything that might be going wrong that I can fix? Regards, Sam

2 1

ChimeraX Boltz prediction running eternally or failing submission to MSA server
by Sam Allen 10 Dec '25

10 Dec '25

Hello, I am currently trying to use ChimeraX Boltz tool to predict the structure of some small ligands onto a GPCR and my prediction running timer just never stops. I initially attempted to install and run the tool on Windows but the install failed to import the mols folder properly multiple times (uninstall and reinstalled), after manually untaring the folder in Powershell it still didn’t run (Timeout while submitting to MSA server). I then decided to switch over to my mac (M1 16GB) and while the install of Boltz in ChimeraX no longer had any error and the prediction didn’t error either, the timer just continued to go up (to 26000 eventually). I figured the protein was too large (471 residues, makes sense), so I tried to rerun one of your test examples (8rf4, https://www.rbvi.ucsf.edu/chimerax/data/boltz-apr2025/runtimes.html) and still no prediction output after 20 minutes. I’ve tried switching from default compute device to GPU or CPU and still no difference. Additionally, in activity monitor it shows ChimeraX is taking up nearly no GPU or CPU usage, so I’m confused as to what is happening. Do you have any advice or know anything that might be going wrong that I can fix? Update: After this email I downloaded the daily ChimeraX version and attempted to run Boltz through that. Instead now the same error as the windows appeared (No authentication provided for MSA server; Failed to process; Skipping. Error: Too many failed attempts for the MSA generation request..) Below is the error in its entirety: Running boltz prediction failed with exit code 0: command: /Users/samuelallen/boltz22/bin/boltz predict /Users/samuelallen/Desktop/boltz_testingtesting123/testingtesting123.yaml --use_msa_server --accelerator gpu --no_kernels stdout: Boltz version 2.2.0 MSA server enabled: https://api.colabfold.com MSA server authentication: no credentials provided Checking input data. Processing 1 inputs with 1 threads. Generating MSA for /Users/samuelallen/Desktop/boltz_testingtesting123/testingtesting123.yaml with 1 protein entities. Calling MSA server for target testingtesting123 with 1 sequences MSA server URL: https://api.colabfold.com MSA pairing strategy: greedy No authentication provided for MSA server Failed to process /Users/samuelallen/Desktop/boltz_testingtesting123/testingtesting123.yaml. Skipping. Error: Too many failed attempts for the MSA generation request.. stderr: 0%| | 0/1 [00:00<?, ?it/s] 0%| | 0/150 [elapsed: 00:00 remaining: ?][A SUBMIT: 0%| | 0/150 [elapsed: 00:00 remaining: ?][AError while fetching result from MSA server. Retrying... (1/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (2/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (3/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (4/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (5/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (6/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) SUBMIT: 0%| | 0/150 [elapsed: 01:04 remaining: ?] Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 534, in _make_request response = conn.getresponse() ^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connection.py", line 571, in getresponse httplib_response = super().getresponse() ^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1395, in getresponse response.begin() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 325, in begin version, status, reason = self._read_status() ^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 286, in _read_status line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py", line 706, in readinto return self._sock.recv_into(b) ^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1314, in recv_into return self.read(nbytes, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1166, in read return self._sslobj.read(len, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TimeoutError: The read operation timed out The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/adapters.py", line 667, in send resp = conn.urlopen( ^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 841, in urlopen retries = retries.increment( ^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/util/retry.py", line 474, in increment raise reraise(type(error), error, _stacktrace) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/util/util.py", line 39, in reraise raise value File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 787, in urlopen response = self._make_request( ^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 536, in _make_request self._raise_timeout(err=e, url=url, timeout_value=read_timeout) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 367, in _raise_timeout raise ReadTimeoutError( urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/data/msa/mmseqs2.py", line 77, in submit res = requests.post( ^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/api.py", line 115, in post return request("post", url, data=data, json=json, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/api.py", line 59, in request return session.request(method=method, url=url, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/sessions.py", line 589, in request resp = self.send(prep, **send_kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/sessions.py", line 703, in send r = adapter.send(request, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/adapters.py", line 713, in send raise ReadTimeout(e, request=request) requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/main.py", line 581, in process_input compute_msa( File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/main.py", line 477, in compute_msa unpaired_msa = run_mmseqs2( ^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/data/msa/mmseqs2.py", line 201, in run_mmseqs2 out = submit(seqs_unique, mode, N) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/data/msa/mmseqs2.py", line 92, in submit raise Exception( Exception: Too many failed attempts for the MSA generation request. 100%|██████████| 1/1 [01:04<00:00, 64.69s/it] 100%|██████████| 1/1 [01:04<00:00, 64.69s/it] GPU available: True (mps), used: True TPU available: False, using: 0 TPU cores HPU available: False, using: 0 HPUs /Users/samuelallen/boltz22/lib/python3.11/site-packages/pytorch_lightning/trainer/connectors/logger_connector/logger_connector.py:76: Starting from v1.9.0, `tensorboardX` has been removed as a dependency of the `pytorch_lightning` package, due to potential conflicts with other packages in the ML ecosystem. For this reason, `logger=True` will use `CSVLogger` as the default logger, unless the `tensorboard` or `tensorboardX` packages are found. Please `pip install lightning[extra]` or one of them to enable TensorBoard support by default Regards, Sam

1 0

Boltz run- Kd values
by Malik, Radhika 08 Dec '25

08 Dec '25

Hello, I am a Research Scientist at Mount Sinai School of Medicine, NY. I have run Boltz in ChimeraX on a protein-ligand complex, however, I am not able to locate the file for the predicted Kd values. Can you please direct me to the file/location? I am attaching a screenshot of what I see after the run. Thanks a lot, Radhika ________________________________ Confidentiality Notice: This electronic mail transmission and any documents, files, or previous email messages attached to it may contain confidential information and are intended solely for the use of the individual or entity to which they are addressed. If you are not the intended recipient, or a person responsible for delivering such information to the intended recipient, you are hereby notified that any further review, disclosure, copying, dissemination, distribution, or use of any of the information contained in or attached to this email transmission is strictly prohibited. If you have received this message in error, please notify the sender immediately by email, discard any paper copies, and delete all electronic files of the message. Thank you for your cooperation.

4 9

NEED HELP TO INSTALL BOLTZ2 in CHIMERAX.
by Dr. V.N. Balaji 07 Dec '25

07 Dec '25

Subject: Bug Report: "Intel Mac" Error Blocking Boltz Install on Windows 11 (NVIDIA 3080 Ti) Dear ChimeraX Team, I am writing to report a platform detection bug in the Boltz installer within ChimeraX (Daily Build 1.12.dev202512040236). When attempting to install Boltz via the boltz install command on a Windows 11 system with a compatible NVIDIA GPU, the installation fails immediately with the following error: "Boltz requires newer Torch versions that are not available on Intel Macs." This appears to be a false positive in the installer's logic, erroneously flagging my Windows/x86_64 system as an unsupported Intel Mac. System Configuration: OS: Windows 11 Pro (x86_64) CPU: Intel Core i9-7940X GPU: NVIDIA GeForce RTX 3080 Ti (12GB VRAM, CUDA 12.x active) ChimeraX Version: 1.12.dev202512040236 (2025-12-04) Context & Troubleshooting: Verified Hardware: I have already successfully installed and verified boltz (v2.2.1) in a standalone PowerShell environment on this same machine; it runs protein-ligand docking with GPU acceleration without issue. Workarounds Attempted: I have tried running ChimeraX in admin mode, using different daily builds, and attempting to manually intervene with pip, but the internal installer aborts before package retrieval begins due to this platform check. Request: Could you advise on a command-line flag or manual workaround to bypass this platform check and force a Windows/CUDA installation? Alternatively, if this requires a patch to the installer script to correctly identify Windows environments, please let me know. Thank you for your assistance. Best regards, V.N. Balaji, Ph.D. Computational Chemist Bangalore, India vnbalaji(a)gmail.com | LinkedIn: vnbalaji

2 2

Can ISOLDE-refined models be directly deposited to the PDB?
by man6ny＠virginia.edu 05 Dec '25

05 Dec '25

Dear all, Maybe an ignorant or previously-asked question... I believe most people refine cryo-EM models using e.g. Phenix real-space-refine before depositing them to the PDB. Is there a strict reason (practical or philosophical) why cryo-EM models refined in ISOLDE cannot be directly deposited without subsequent refinement in Phenix or Refmac? I have a high-resolution map (2.2 A) but the latter programs seem to actually make my model worse (e.g. Phenix tends to give me rotamers that are not supported by the experimental data). I would prefer to use the model refined in ISOLDE but perhaps I am missing something? Many thanks for your insight! Louis

4 4

Opening multiple chimeraX windows at the same time?
by Choy, Jon 05 Dec '25

05 Dec '25

Hi Oliver and Tom or whom it may concern, I was interested in whether it is possible to open multiple .cxs files at the same time? I am comparing structural features across many different proteins and their corresponding maps—and it is very annoying to be only able to open one map and its protein at a time. Although it is possible to load multiple resolved structures and their maps into a single .cxs file, these structures all load onto different spots on the chimeraX interactive space—making side by side comparison a bit cumbersome. Assistance in this would be massively appreciated! Thank you so much and looking forward to hearing from you. Best, Jon

3 2

Calcium ions labeled as solvent, not as ions
by Ute Roehrig 05 Dec '25

05 Dec '25

Hello, I am not sure if this is a problem in the structure or in ChimeraX or intentional, but I remarked that in PDB structure 7tba the calcium ions are labeled as "solvent" and not as "ions", although the element and atom type seem to be OK. I did not see the same in other PDB structures with calcium. Thank you for your help, Ute

3 4

Subject: Request for Detailed Clarification on ChimeraX RMSD, Alignment Metrics, and Pruning Calculations
by EMMANUEL JAIME SIBAYAN 05 Dec '25

05 Dec '25

Hello, Good day. I am using ChimeraX for an academic research project involving protein structure comparison. Before proceeding with my analysis, I would like to request detailed clarification on how ChimeraX obtains specific structural comparison values. In particular, I would like to understand: how ChimeraX gets these values and what formulas or computational methods are used for each measurement. Specifically, I would like to ask about the following: 1. The recommended procedure for computing RMSD between two protein structures in ChimeraX, including the appropriate steps, commands, and settings to ensure a correct and reproducible measurement. 2. How ChimeraX determines aligned residue pairs during Matchmaker or similar alignment tools, including how residues are selected or excluded based on sequence alignment and structural fit. 3. The exact meaning and calculation method for “pruned atom pairs” in the alignment results. In particular, I would like clarification on the pruning process (for example, removal of atom pairs whose distances exceed a threshold) and how this affects the final reported values. 4. Whether RMSD in ChimeraX is calculated using all aligned atom pairs, pruned atom pairs only, or whether both values are available. I would also like to understand how to correctly interpret RMSD before pruning versus RMSD after pruning. 5. How ChimeraX performs structural alignment when the two sequences are identical but the predicted models have local deviations such as altered loops, turns, flexible regions, or insertions. 6. Recommended best practices when comparing three types of structures: • an experimental PDB crystal structure • an AlphaFold predicted structure • a Swiss-Model homology model 7. Any documentation, reference materials, or example workflows that explain the statistical reporting of structural comparison in ChimeraX, especially the following values: • RMSD, calculated as √(1/N Σ di²) • distance measurements between paired atoms, defined as √[(x1 − x2)² + (y1 − y2)² + (z1 − z2)²] • aligned residue counts • pruning thresholds and post-pruning atom pair counts This information will help ensure that the statistical evaluation in my study (including RMSD, aligned residues, and pruned atom pairs) is methodologically correct and consistent with ChimeraX standards. Thank you very much for your time and assistance. Your guidance will greatly improve the accuracy and reliability of my research analysis. Best regards, [Your Name] -- *The information or attachment(s) in this email is(are) strictly confidential and is(are) for the intended recipient only. Any unauthorized use, dissemination, or copy of this message or the information it contains is prohibited. The recipient has the responsibility to ensure the protection of any personal data included in this e-mail and its attachment(s). If you are not the intended recipient or you receive this email by mistake, please notify the sender immediately and delete the original message and attachment(s).*

2 1

Recording High Quality MD Trajectory Movie in ChimeraX
by Gourav Das 03 Dec '25

03 Dec '25

Dear ChimeraX users, I am recording the MD trajectory of a simulation as a movie in ChimeraX. However, the output quality of the movie is very low. How can I improve the quality of the movie? I would appreciate your guidance regarding this issue. Thank you for your support. With regards, Gourav Das Research Scholar Indian Institute of Technology Kharagpur West Bengal, India-721302 Mob: +91-6295251060 --

2 2

RHEL/Rocky/AlmaLinux/etc 10 releases available
by Greg Couch 03 Dec '25

03 Dec '25

We are pleased to announce that you can now get 1.11 release candidates and daily builds for Red Hat Enterprise Linux 10 and derivatives. For example, Rocky 10 and AlmaLinux 10. A more complete list can be found on wikipedia, https://en.wikipedia.org/wiki/Red_Hat_Enterprise_Linux_derivatives. Since this is a new platform for ChimeraX, it hasn't been tested as thoroughly as the other platforms. We expect the RHEL 10 releases to be bug-for-bug compatible with the RHEL 9 releases, but there is a chance that they aren't. So please try one out and report any bugs you find. -- Greg

1 0

Colouring Amino Acids Within A Selected Region
by Nusrat Tazkia 03 Dec '25

03 Dec '25

Hello ChimeraX developpers, I hope you are doing well. I was trying to colour each amino acid present within a selected region of my model and couldn't figure out how to do it. Could you please guide me on how to do it? I ran these commands (for examples for chains A and E) and have attached my model in this email as well: interfaces select /A contacting /E bothSides true color sel red Please let me know at your earliest convenience. Thank you, Nusrat Tazkia

2 5

How to measure the correlation length of a map in ChimeraX
by 张楠 02 Dec '25

02 Dec '25

Dear ChimeraX Developers, I have an EM density map and need to measure its diameter and height. I used the "measure and color blob" tool, which displays the length, width, and height of the entire EM density when clicked. However, the values are measured around the entire density map, making them slightly larger than the actual diameter. Therefore, I tried using the "tape" tool to measure, but it is difficult to select two perfectly horizontal points for an accurate measurement. I would like to ask how to measure the correlation length of a map in ChimeraX. Looking forward to your answer, thank you! Best regards, Nan Nan Zhang zhangnan(a)nankai.edu.cn

2 1

Alpha-fold-chimerax-coot - incompatibility
by Abhilash Padavannil 01 Dec '25

01 Dec '25

Hi All, I am having trouble with .cif files in Chimerax — I re-built the model (Model-Angelo) in coot using alpha-fold models for completion and saved it as a .cif file. When I open the file in Chimerax certain proteins in the complex show up differently and the their chain IDs are missing in the Chimerax list. Could you help me fix this ? Previously I was able to combine the individual alpha-fold models to a single in Chimerax .cif file. However, if I do local refinement in coot the chains go back to being different. Please suggest. Attached is the screen shot for reference. Thank you. [cid:d13d01b7-12bf-4117-8bbe-f63d6679629a@namprd08.prod.outlook.com]

3 2

GPU/CUDA support for toolshed deep learning plugin
by HAWICKHORST, BRYAN 01 Dec '25

01 Dec '25

Hello, I am a student from Professor Jing He's lab at Old Dominion University. I am trying to enable GPU acceleration for our deep learning plugin, DeepSSETracer. The problem I am running into is that python in the chimerax environment cannot see cuda. Varying cuda versions seems to rule out including cuda as a dependency. Additionally, we would like to avoid custom cuda installations via the chimerax terminal, as it would greatly complicate installation for the users of our plugin. Is there a way to support cuda or GPU acceleration in another way (that ideally does not require user interaction with the chimerax terminal)? Or, could you point me towards tools that have managed to do this? I found this library, ONNX Runtime and wonder if it may be useful: https://onnxruntime.ai/docs/get-started/with-python.html#install-onnx-runti… Best regards, Bryan Hawickhorst Old Dominion University

2 1

Permission to create winget manifest?
by Joshua Raphael Uy 25 Nov '25

25 Nov '25

Hi Chimerax Dev team, My name is Josh Uy. I'm a graduate student at Arizona State University, and I frequently use ChimeraX as a visualization tool on both Windows and Linux! I'm wondering if you guys would be ok if I were to submit a winget <https://github.com/microsoft/winget-cli> manifest for ChimeraX? ChimeraX is a wonderful piece of software that I am using for my Ph.D and having an automated way to get and install via cli package manager tools would be incredibly handy to have. I wouldn't mind being the guy responsible for maintaining this if approved. Thank you, Josh Uy

2 1

Unable to restore session: need to install missing bundle
by GOVAERTS Cédric 25 Nov '25

25 Nov '25

Hi Team, I’m switching between computers and platforms, but now I try to reopen CXS session it fails and I get To restore session: install Animations bundle version 1.0 or newer Unable to restore session: need to install missing bundle I’ve tried the very last version of chimeraX (daily built). How can I solve this ? Thanks a bunch Cedric Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77<tel:+3226505377> Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

2 5

command history pulldown very short
by Alan Cheung 25 Nov '25

25 Nov '25

Hi There - i’m using chimerax on mac. Whenever i try to view my command history, either by tapping the up cursor or using the pop-out window, i can only ever recall 16 previous commands despite being set to remember 500 commands. However, the command file in ~/Library/Application Support/ChimeraX/commands contains (at least) 500 commands. Can you help? Alan

2 4

Unable to install boltz - please help
by Aggarwal, Aneel 25 Nov '25

25 Nov '25

Hello, I am a new user and trying to use boltz on my iMac (Tahoe OS) and get the error below. Any suggestions? Thanks, Aneel Successfully created Boltz Python virtual environment /Users/aneel/boltz22. Now installing Boltz and required packages from PyPi. This may take tens of of minutes since Boltz uses many other packages totaling about 1 Gbyte of disk space including torch, scipy, rdkit, llvmlite, sympy, pandas, numpy, wandb, numba... /Users/aneel/boltz22/bin/python -m pip install https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip Collecting https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip Using cached https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' INFO: pip is looking at multiple versions of boltz to determine which version is compatible with other requirements. This could take a while. ERROR: Could not find a version that satisfies the requirement torch==2.7.1 (from boltz) (from versions: 2.0.0, 2.0.1, 2.1.0, 2.1.1, 2.1.2, 2.2.0, 2.2.1, 2.2.2) ERROR: No matching distribution found for torch==2.7.1 [notice] A new release of pip is available: 24.0 -> 25.3 [notice] To update, run: /Users/aneel/boltz22/bin/python -m pip install --upgrade pip Boltz installation failed. See ChimeraX Log for details

3 5

Activation webcam macos sequoia MacBookAir M3 CimeraX 1.10
by GIUSEPPE DOMENICO TOCCHINI VALENTINI 25 Nov '25

25 Nov '25

Hello, I am trying to activate the webcam but I get the following message: [Screenshot 2025-11-25 alle 15.53.15.png] The application does not appear on the camera preferences/privacy. Do you have any suggestion? Thank you in advance. Giuseppe

2 1

Fwd: Boltz predictions and SMILES
by Eric Pettersen 25 Nov '25

25 Nov '25

> Begin forwarded message: > > From: Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> > Subject: RE: Your message to chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> awaits moderator approval > Date: November 25, 2025 at 8:19:02 AM PST > To: "chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>" <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> > > > Hi Guys, > This is about the behavior of smiles uploaded for boltz predictions. Some of the small molecule structures are incorrect after the predictions. My cyclohexyl ring was flattened to a benzene like ring; my protonated amine group in a benzyl amine ended up looking like a cyano group. Anything we can do about it? > Thanks > Krish > CONFIDENTIALITY NOTICE > > This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >

2 1

Re: Problem with modeller execution location
by Alexandra Zahradnikova 24 Nov '25

24 Nov '25

Dear Vinita Now I see that the window I mentioned is not present when you run Modeller from your computer. Maybe you should first try a computation with the web service? I have never used a local installation of the Modeller. The licence key may bi different when working from inside ChimeraX. Best Sasha From: Alexandra Zahradnikova [mailto:alexandra.zahradnikova@savba.sk] Sent: Monday, November 24, 2025 10:13 To: 'Vinita Pant' Cc: chimerax-users(a)cgl.ucsf.edu Subject: RE: [chimerax-users] Re: Problem with modeller execution location Dear Vinita, In the menu item Structure Prediction/Model Loops or Modeller Comparative there are boxes in which you insert the license key (password) – see the screenshots. Best regards Sasha From: Vinita Pant [mailto:vinipant78@gmail.com] Sent: Saturday, November 22, 2025 18:26 To: Alexandra Zahradnikova Subject: Re: [chimerax-users] Re: Problem with modeller execution location Thank you for your response. However, I did not find any option to input the MODELLER password. Since I am not very tech-savvy, could you please guide me? Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943 On Sat, 22 Nov 2025 at 21:22, Alexandra Zahradnikova <alexandra.zahradnikova(a)savba.sk> wrote: Dear Vinita, You have to input the MODELLER password into the ChimeraX interface before starting the program. You will get the password by e-mail when you register with the Modeller web-page. Best Sasha From: Vinita Pant via ChimeraX-users [mailto:chimerax-users@cgl.ucsf.edu] Sent: Saturday, November 22, 2025 15:43 To: ChimeraX Users Help Subject: [chimerax-users] Re: Problem with modeller execution location Dear Elaine, I also tried reinstalling Modeller. But the problem persists. I have attached the image showing the error. Is there a way to manually fix this in Chimera? Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943 On Tue, 18 Nov 2025 at 22:41, Vinita Pant <vinipant78(a)gmail.com> wrote: Thank you for the clarification. Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943 On Tue, 18 Nov 2025, 10:39 pm Elaine Meng, <meng(a)cgl.ucsf.edu> wrote: The errror message is not about the path/location. It is about the license key, which you have to enter into the dialog directly. Please read the help: > https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html#key If you can't find the key in your local installation just follow the instructions/links in the above to get another key from the Modeller developers. Elaine > On Nov 18, 2025, at 8:59 AM, Vinita Pant via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Thank you for the information. Yes I have been using the academic version of Modeller directly. I tried locating the modeller path inside chimera. It still didn't work. > > Thanks and Regards > Vinita Pant > Doctoral Student (SRF) > ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal > Mobile No.: +91 9536940943 > > On Tue, 18 Nov 2025, 10:26 pm Elaine Meng, <meng(a)cgl.ucsf.edu> wrote: > Hi Vinita, > This error message is not about the location. As it says in the message, you have to get a license key for Modeller, which is obtained from the Modeller developers. > > This is all explained in the documentation, e.g. shown by clicking the Help button on the Model Loops dialog. See requirement #3 in the documentation: > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html#key> > > You would need to enter that license key into the tool as described. When you say "successfully using Modeller for homology modeling" I don't know if you meant from inside ChimeraX, or just using Modeller directly. If you were doing it from inside ChimeraX, you should have already gotten this license key and entered it into the ChimeraX dialog. If you were doing it directly with Modeller installed on your own computer, I don't know where the license key is kept. Probably somewhere in the Modeller installation. > > 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 Nov 17, 2025, at 11:04 PM, Vinita Pant via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Dear ChimeraX Team, > > I am using ChimeraX (version: 1.10.1 (2025-07-24)) for filling missing residues, for which Chimera uses Modeller in the background. However, I've encountered an issue regarding the executable location of Modeller. Although I am successfully using Modeller for homology modeling, I am receiving a notification in ChimeraX stating that the license key is unavailable. I have attached an image of the error message for your reference. > > I would appreciate your guidance in resolving this matter. > > > > Thanks and Regards > > Vinita Pant > > Doctoral Student (SRF) > > ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal > > Mobile No.: +91 9536940943 > > _______________________________________________ > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

3 2

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24 Nov '25

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2 1

Re: Problem opening local small-molecule CIF file
by Starborg, Toby (RFI,RAL,BPSUP) 24 Nov '25

24 Nov '25

Oh dear. Sorry Ute, I'm afraid that I miss-read your original email. I was using the command open:ccd pim, which, I've just realised, you said worked. Sorry for the confusion. Out of interest where did you download the PIM.cif file and I will try opening it in the GUI. TobyS ________________________________ From: Ute Roehrig <Ute.Roehrig(a)sib.swiss> Sent: 24 November 2025 10:30 To: Starborg, Toby (RFI,RAL,BPSUP) <tobias.starborg(a)rfi.ac.uk> Subject: Re: Problem opening local small-molecule CIF file This is an external email. Please take care when clicking links or opening attachments. When in doubt, contact the helpdesk. Hi Toby, Which command is working for you? "open PIM.cif" does not work for me on linux/version 1.11.dev2025*, linux/version 1.10, macOS Tahoe/version 1.11.dev2025*, macOS Tahoe/version 1.10.1 Thanks, Ute ________________________________ From: Starborg, Toby (RFI,RAL,BPSUP) <tobias.starborg(a)rfi.ac.uk> Sent: Monday, November 24, 2025 10:56 To: Mailing List <chimerax-users(a)cgl.ucsf.edu>; Ute Roehrig <Ute.Roehrig(a)sib.swiss> Subject: Re: Problem opening local small-molecule CIF file Hi Ute, I'm by no means an expert, but I just tried the same command and it worked fine for me. Perhaps you need to expand the info to include what version of ChimeraX you are using and on what system? [FYI, I'm using version 1.10 on a Macbook Pro running Sequoia 15.7.1). TobyS ________________________________ From: Ute Roehrig via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Sent: 24 November 2025 09:49 To: Mailing List <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] Problem opening local small-molecule CIF file This is an external email. Please take care when clicking links or opening attachments. When in doubt, contact the helpdesk. Hello, I'm having problems opening a locally stored small-molecule cif file. For example, the following runs without problems: open ccd:pim But if I download the file (PIM.cif) and try to open it with ChimeraX, I get an error: open PIM.cif -> No mmCIF models found. open PIM.cif format corecif -> No small molecule CIF models found. Perhaps this is a mmCIF file? open PIM.cif format smallcif -> No small molecule CIF models found. Perhaps this is a mmCIF file? Thank you in advance for your help, Ute

1 0

Problem opening local small-molecule CIF file
by Ute Roehrig 24 Nov '25

24 Nov '25

Hello, I'm having problems opening a locally stored small-molecule cif file. For example, the following runs without problems: open ccd:pim But if I download the file (PIM.cif) and try to open it with ChimeraX, I get an error: open PIM.cif -> No mmCIF models found. open PIM.cif format corecif -> No small molecule CIF models found. Perhaps this is a mmCIF file? open PIM.cif format smallcif -> No small molecule CIF models found. Perhaps this is a mmCIF file? Thank you in advance for your help, Ute

2 1

Re: Problem with modeller execution location
by Alexandra Zahradnikova 24 Nov '25

24 Nov '25

Dear Vinita, In the menu item Structure Prediction/Model Loops or Modeller Comparative there are boxes in which you insert the license key (password) – see the screenshots. Best regards Sasha From: Vinita Pant [mailto:vinipant78@gmail.com] Sent: Saturday, November 22, 2025 18:26 To: Alexandra Zahradnikova Subject: Re: [chimerax-users] Re: Problem with modeller execution location Thank you for your response. However, I did not find any option to input the MODELLER password. Since I am not very tech-savvy, could you please guide me? Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943 On Sat, 22 Nov 2025 at 21:22, Alexandra Zahradnikova <alexandra.zahradnikova(a)savba.sk> wrote: Dear Vinita, You have to input the MODELLER password into the ChimeraX interface before starting the program. You will get the password by e-mail when you register with the Modeller web-page. Best Sasha From: Vinita Pant via ChimeraX-users [mailto:chimerax-users@cgl.ucsf.edu] Sent: Saturday, November 22, 2025 15:43 To: ChimeraX Users Help Subject: [chimerax-users] Re: Problem with modeller execution location Dear Elaine, I also tried reinstalling Modeller. But the problem persists. I have attached the image showing the error. Is there a way to manually fix this in Chimera? Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943 On Tue, 18 Nov 2025 at 22:41, Vinita Pant <vinipant78(a)gmail.com> wrote: Thank you for the clarification. Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943 On Tue, 18 Nov 2025, 10:39 pm Elaine Meng, <meng(a)cgl.ucsf.edu> wrote: The errror message is not about the path/location. It is about the license key, which you have to enter into the dialog directly. Please read the help: > https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html#key If you can't find the key in your local installation just follow the instructions/links in the above to get another key from the Modeller developers. Elaine > On Nov 18, 2025, at 8:59 AM, Vinita Pant via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Thank you for the information. Yes I have been using the academic version of Modeller directly. I tried locating the modeller path inside chimera. It still didn't work. > > Thanks and Regards > Vinita Pant > Doctoral Student (SRF) > ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal > Mobile No.: +91 9536940943 > > On Tue, 18 Nov 2025, 10:26 pm Elaine Meng, <meng(a)cgl.ucsf.edu> wrote: > Hi Vinita, > This error message is not about the location. As it says in the message, you have to get a license key for Modeller, which is obtained from the Modeller developers. > > This is all explained in the documentation, e.g. shown by clicking the Help button on the Model Loops dialog. See requirement #3 in the documentation: > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html#key> > > You would need to enter that license key into the tool as described. When you say "successfully using Modeller for homology modeling" I don't know if you meant from inside ChimeraX, or just using Modeller directly. If you were doing it from inside ChimeraX, you should have already gotten this license key and entered it into the ChimeraX dialog. If you were doing it directly with Modeller installed on your own computer, I don't know where the license key is kept. Probably somewhere in the Modeller installation. > > 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 Nov 17, 2025, at 11:04 PM, Vinita Pant via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Dear ChimeraX Team, > > I am using ChimeraX (version: 1.10.1 (2025-07-24)) for filling missing residues, for which Chimera uses Modeller in the background. However, I've encountered an issue regarding the executable location of Modeller. Although I am successfully using Modeller for homology modeling, I am receiving a notification in ChimeraX stating that the license key is unavailable. I have attached an image of the error message for your reference. > > I would appreciate your guidance in resolving this matter. > > > > Thanks and Regards > > Vinita Pant > > Doctoral Student (SRF) > > ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal > > Mobile No.: +91 9536940943 > > _______________________________________________ > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

1 0

Problem with modeller execution location
by Vinita Pant 22 Nov '25

22 Nov '25

Dear ChimeraX Team, I am using ChimeraX (version: 1.10.1 (2025-07-24)) for filling missing residues, for which Chimera uses Modeller in the background. However, I've encountered an issue regarding the executable location of Modeller. Although I am successfully using Modeller for homology modeling, I am receiving a notification in ChimeraX stating that the license key is unavailable. I have attached an image of the error message for your reference. I would appreciate your guidance in resolving this matter. *Thanks and Regards* *Vinita Pant* *Doctoral Student (SRF)* *ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal* *Mobile No.: +91 9536940943*

3 6

Chimera X with Apple Vision Pro
by Wolf, Inga 21 Nov '25

21 Nov '25

Dear Chimera X and Chimera developers, I'm a staff member of the Max-Planck-Institute of Biochemistry near Munich, Germany. At the moment we use Vive Pro virtual glasses to create a 3D picture of our biological structures that have extensions to be showed in Chimera X (.wrl, .mrc ...). Chimera X and the glasses can be connected. Vive Pro is now 8 years old and we think of buying Apple Vision Pro glasses. Can you please tell me if Chimera X or Chimera can talk to these glasses? Is there a possibility to see the structures in these glasses? Thank you in advance for your answer. Best regards, Inga Wolf Inga Wolf Cell and Virus Structure John Briggs [1685544407897] MAX PLANCK INSTITUTE OF BIOCHEMISTRY Am Klopferspitz 18 | 82152 Martinsried | Germany Phone: +49 (89) 8578 - 2634 iwolf(a)biochem.mpg.de<mailto:name@biochem.mpg.de> http://www.biochem.mpg.de/briggs<http://www.biochem.mpg.de/>

2 1

Predicting and modeling post-translationally modified C-terminal endings
by Parks, Ryssa 21 Nov '25

21 Nov '25

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

4 9

Navigating to a OneDrive folder prompts a wholesale download
by David Bhella 20 Nov '25

20 Nov '25

Dear ChimeraX users and team, I am wondering if anyone can advise how to stop OneDrive trying to download the contents of every folder I navigate through when trying to e.g. save an image or open a file? I haven’t seen this behaviour with any other software, but as I maintain a lot of my work on OneDrive, it would be nice to be able to interact directly with the working folder. At the moment I need to work on a local folder and then copy files across when saving, and open files through finder rather than the ChimeraX dialog, otherwise my Mac locks up while it tries to download everything in every folder it sees. Thanks, D David Bhella Professor of Structural Virology Director, Scottish Centre for Macromolecular Imaging Associate Director, MRC - University of Glasgow Centre for Virus Research +44 (0)141 330 3685<tel:+441413303685> [cid:image002.png@01DAE420.99202CC0] [Logo, company name Description automatically generated]

2 1

AI spam
by Eric Pettersen 18 Nov '25

18 Nov '25

Hi all, We have made some further adjustments to try to prevent these AI spams posts you have seen over the last few days. We are hopeful, but you never can be sure... --Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

ChimeraX languages
by Nicolas Caudron - IA-IPR SVT 18 Nov '25

18 Nov '25

2 1

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18 Nov '25

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1 0

Listing cavity contacting residues
by George Tzotzos 17 Nov '25

17 Nov '25

Hi everyone, I’ve used kvfinder and the command: coulombic (#1 & protein) surfaces #1.1.1 offset -1 select #!1 & (#!1.1.1 @< 3.5)185 atoms, 163 bonds, 34 residues, 1 model selected Is there a way to list the 34 residues? Have a good day George

2 2

Colouring a morph anim
by Pranav Shah 17 Nov '25

17 Nov '25

Hi Team, I am seeking advice on the most effective way to visualize a morphing trajectory within ChimeraX. Specifically, I have a multi-chain model transitioning (morphing) from its starting state to its final state, and I would like to know if there is a method in ChimeraX to apply a color gradient along this trajectory. Additionally, I would greatly appreciate guidance on how to color specific atoms, such as Cα atoms, based on their overall displacement. Ideally, the color intensity (hue) would increase in proportion to the magnitude of the displacement. Best regards, Pranav 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

2 2

Converting .stl to .mrc or .pdb
by mitchell.gulkis＠ufl.edu 17 Nov '25

17 Nov '25

Hello everyone, For instructional purposes, I am trying to generate simulated cryo-EM micrographs from a .stl file, in this case Mickey Mouse. This way, students can hold the 3D printed Mickey up to the micrograph to better understand projection images and angular assignment. I am able to open the .stl file in ChimeraX, but I can not figure out how to convert it to a format that is accepted by micrograph simulation programs, either .mrc or .pdb. Has anyone else figured out how to do this? Thanks! Sincerely, Mitch

4 3

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PyPI Chimerax Package for Windows
by Berenice E Cowfer Chavez 14 Nov '25

14 Nov '25

Hello, Do you have a PyPI ChimeraX package for windows? I can online find a .whl file for macOS. Sincerely, Berenice E. Cowfer Chavez, M.S. Lab Manager, Profs. Johnson and Shoulders Labs Massachusetts Institute of Technology

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A fixed clipping plane?
by jon_choy＠g.harvard.edu 14 Nov '25

14 Nov '25

Hi all, Prior to this I was an avid IMOD user. There I was able to set a clipping plane and move/rotate the model such that the model clipping plan would NOT clip any other parts of the model. Essentially i want to create a clipping plane, set it and then transform the model such that no other parts of the model will be clipped. Is this possible? I could not figure it out for the life of me. It's pretty simple in IMOD, just not sure if it's possible in ChimeraX. Would love to hear what you guys think. -Jon

4 6

color of capped surface
by stokes＠nyu.edu 12 Nov '25

12 Nov '25

I am having trouble with the surface color and specifically of capped surfaces. To start, surfaces of individual chains are given a single color, despite individual domains having been assigned a variety of colors. I can change the colors of the surface for individual domains subsequently, so that is not so bad. However, the color of the capped surface remains the initial color adopted when the surface was created. When I change colors of the individual chains, or domains, the surface color changes, but not the color of the capped/clipped surface. If I change the color of the entire model, then the surface cap changes. But it does not respond to subsequent changes of individual chains and domains. Hiding/showing the surface does not solve the problem (though I have a dim memory of this working in the past - maybe that was the old chimera). I am only using near/far clipping planes - not front/back. ChimeraX 1.10.1 on Ubuntu and 1.8 on Windows behave the same. Thanks in advance for any insight, David

2 2

Blurry Volume Rendering in ChimeraX ≥1.7 on macOS (HiDPI Regression Affecting ArtiaX)
by Yaroslav Tsytsyura 11 Nov '25

11 Nov '25

A little comment to the message: The following text was generated with help of an AI, because I’ve got frustrated trying to solve the issue myself and ran out of strength; I apologise for that. Yet it describes the problem well: Dear ChimeraX/ArtiaX developers, I would like to report an issue with volume rendering quality on macOS that appears to have been introduced in ChimeraX versions 1.7 and later, and that affects ArtiaX-based tomography workflows. System details macOS 26.0.1 on Apple Silicon (M2 Pro; RAM 16GB) ChimeraX 1.6.1 (works correctly) ChimeraX 1.7–1.10.1 (affected) ArtiaX 0.3 (works correctly) ArtiaX 0.6 (affected) Native ARM64 ChimeraX binary used (not via Rosetta) Tested both on the built-in display and external 4K monitor Issue summary When displaying reconstructed tomograms (binned 4x to pixel value 10A) in ChimeraX 1.7 and newer, the volume appears blurry, pixelated, and significantly lower in resolution compared to Fiji or ChimeraX 1.6.1. The same tomogram, same hardware, same display settings, and same scaling factors show correct high-quality sampling in ChimeraX 1.6.1 + ArtiaX 0.3. In contrast, ChimeraX ≥1.7 + ArtiaX ≥0.6 consistently produce a downsampled-looking rendering. Troubleshooting performed To rule out common macOS/Qt/HiDPI issues, I have tested: Forcing HiDPI mode (QT_ENABLE_HIGHDPI_SCALING, QT_SCALE_FACTOR, etc.) Launching via arch -arm64 Removing and reinstalling ChimeraX completely (including preferences) Disabling external 4K monitor scaling Resetting ChimeraX user settings None of these affected the outcome. Only reverting ChimeraX to version 1.6.1 restores correct rendering quality. Behavior differences observed In ChimeraX 1.6, tomograms appear crisp and match Fiji’s display quality. In ChimeraX 1.7–1.10.1, the same tomograms appear visibly blurred and pixelated. The command graphics quality high or similar parameters appear unsupported or ineffective in newer versions. ArtiaX toolbar loads but seems to use lower-resolution textures for slice volumes. This strongly suggests a rendering pipeline change around the transition from ChimeraX 1.6.1 → 1.7 that affects ArtiaX’s volume display on macOS (possibly due to Qt scaling, offscreen framebuffer size, or texture sampling changes). Request Could you please check whether: ArtiaX 0.6 is triggering half-resolution internal textures on macOS? The new rendering pipeline introduced in ChimeraX ≥1.7 affects HiDPI texture sampling? There is a fallback path on macOS ARM that reduces framebuffer resolution? Any configuration options can restore full-resolution sampling? To illustrate the difference between the two options (ChimeraX 1.6 vs 1.10.1) I have included the snapshots from two different M2 MacBooks running two different versions of ChimeraX/ArtiaX combinations; the tomogram file, tomogram optical slice position are the same, the screen magnification and the regions displayed are very similar. Thank you very much for your work and for looking into this. Best regards, Yaroslav ------------------------------------------- Dr. Yaroslav Tsytsyura Cellular Biophysics Institute of Medical Physics and Biophysics University of Muenster Robert-Koch Str., 31 48149, Muenster GERMANY phone: +49 251 8351 010 fax: +49 251 8355 121 Mobile: +49 157 895 47789 web-page: https://www.medizin.uni-muenster.de/impb/das-institut/elektronenmikroskopie…

2 2

Offscreen/headless render acceleration
by Roden Deng Luo 07 Nov '25

07 Nov '25

Hi, In https://www.cgl.ucsf.edu/chimerax/docs/user/options.html, under `--offscreen`, it says "It cannot use a graphics card or hardware-accelerated rendering because OpenGL does not support rendering without a window." I wonder if there are any possible ways to utilize graphics cards in the headless mode, or if you have any best practices for saving pictures/movies for hundreds to thousands of structures, with or without a GUI. Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

2 2

front-back shadow
by Citterico, Matteo 07 Nov '25

07 Nov '25

Hello, I’m having trouble changing the depth cue start and end settings in ChimeraX 1.8. I’ve tried several commands, but none of them seem to work. Could you please help me with this? Thank you in advance, Matteo

5 6

Recent spam
by Eric Pettersen 06 Nov '25

06 Nov '25

It seems that the era of AI bots signing up for and posting to mailing lists is upon us. I have banned the email address of the recent spam source and we are investigating methods to prevent these kinds of sign-ups/posts in the future. --Eric Eric Pettersen UCSF Computer Graphics Lab

2 1

The House Always Wins
by johncarry9t＠gmail.com 06 Nov '25

06 Nov '25

The word "casino" conjures specific imagery: the clinking of chips, the hypnotic spin of the roulette wheel, the electric chorus of a slot machine jackpot. For centuries, these establishments have been temples of chance, promising glamour, excitement, and the life-changing possibility of a big win. But behind the flashing lights and free-flowing cocktails lies a meticulously engineered ecosystem designed for one ultimate goal: profitability. The modern casino is a fascinating blend of psychology, architecture, technology, and entertainment, far removed from the smoky, simplistic gambling halls of the past. https://hamiltongardens.org/visit/ The Architecture of Addiction: Designed to Disorient From the moment you step inside, the casino environment is carefully crafted to keep you playing. There are no clocks or windows, creating a timeless bubble where the outside world ceases to exist. Labyrinthine floor plans encourage exploration and make it difficult to find the exit. The air is oxygenated to keep patrons alert, and the constant sensory stimulation—from the ringing of slots to the vibrant carpet patterns—creates an atmosphere of thrilling chaos. This design is no accident. It's a calculated strategy to maximize "time on device." The longer a guest stays, the more the mathematical advantage of the games, known as the "house edge," grinds down their bankroll. Every element, from the placement of popular slots to the complimentary "comps" like drinks and hotel rooms, is a tool to enhance customer retention. The Games: A Calculated Dance of Chance At its core, a casino's business model is a masterpiece of applied mathematics. Every game offered is statistically tilted in the house's favor. Slot Machines: The undisputed king of the casino floor, slots are now sophisticated computers. Their outcomes are determined by Random Number Generators (RNGs), and their payout percentage, or "Return to Player" (RTP), is programmed in advance. Their appeal lies in their simplicity and the potential for massive, albeit infrequent, jackpots. Table Games: Games like Blackjack, Roulette, and Baccarat offer more player agency, but the house edge is immutable. In Blackjack, the dealer plays by fixed rules that disadvantage the player over time. In Roulette, the presence of the "0" and "00" on the American wheel gives the house its built-in advantage. Craps and Baccarat operate on similar statistical principles. Despite the odds, these games thrive because they offer the illusion of control and the social spectacle of a live game, presided over by a skilled dealer. Beyond the Floor: The Rise of the Integrated Resort The 21st-century casino is rarely just a casino. The model of the "Integrated Resort" has transformed these venues into full-scale entertainment destinations. Today's major casinos are home to: World-class hotels and spas Celebrity-chef restaurants High-end retail shopping Arena-sized theaters hosting A-list performers Convention and meeting spaces This diversification is a strategic move. By attracting conventioneers, gourmands, and concert-goers who may not be primary gamblers, resorts ensure a steady revenue stream that isn't solely dependent on the volatility of the gaming floor. It normalizes the casino, repositioning it as a legitimate vacation spot for a broader demographic. The Digital Frontier: Online Casinos and the Future The most significant shift in recent years has been the explosive growth of online casinos and mobile sports betting. The digital realm removes all physical barriers, allowing people to gamble from their living rooms or on their phones. This presents both immense opportunity and significant challenges. Online platforms use sophisticated algorithms and bonus structures to engage players, often with even higher efficiency than their brick-and-mortar counterparts. This accessibility has intensified the focus on responsible gambling. Regulators and ethical operators are now implementing tools like deposit limits, "cool-off" periods, and self-exclusion programs to help mitigate the risks of addiction that are amplified in the always-available online environment. The Final Bet The modern casino is a complex entity. It is a source of employment, tourism revenue, and entertainment for millions. It is also a highly engineered environment that profits from human psychology and mathematical certainty. As the industry continues to evolve with technology and expand into new markets, the balance between entertainment, profit, and social responsibility remains its defining tension. The house may always win in the end, but understanding the intricate machinery behind the magic curtain is the most valuable bet a visitor can make.

1 0

F8BET Payment Methods
by johncarry9t＠gmail.com 06 Nov '25

06 Nov '25

A seamless banking experience is F8BET essential for any online casino player. F8BET provides a variety of safe, fast, and convenient payment methods, ensuring that deposits and withdrawals are hassle-free. Whether you prefer credit cards, e-wallets, or cryptocurrencies, F8BET guarantees secure transactions so you can focus on gaming. https://f8betlv.com/ Why Payment Methods Matter Efficient payment options enhance your online casino experience by: Saving Time: Quick deposits and withdrawals mean more gameplay. Providing Security: Advanced encryption protects your financial information. Offering Flexibility: Multiple options cater to different player preferences. Enabling Bonuses: Many payment methods qualify for deposit promotions. Deposit Options at F8BET F8BET offers multiple deposit methods for player convenience: 1. Credit and Debit Cards Visa, MasterCard, and Maestro are widely accepted. Instant deposits with secure processing. Tip: Ensure your card is enabled for online transactions. 2. E-Wallets Options include Skrill, Neteller, and ecoPayz. Quick deposits with added privacy. Tip: Some e-wallets offer cashback or promotions when depositing. 3. Bank Transfers Direct transfers from your bank account. Reliable and secure, though processing may take longer than e-wallets. 4. Cryptocurrencies Bitcoin, Ethereum, and other popular cryptocurrencies are accepted. Fast and secure with added anonymity. Tip: Check current exchange rates to maximize your deposit value. Withdrawal Methods F8BET ensures smooth and Đăng ký F8BET timely withdrawals: https://f8betlv.com/ E-Wallets: Typically processed within 24 hours. Bank Transfers: May take 2-5 business days depending on your bank. Credit/Debit Cards: Usually processed within 1-3 business days. Cryptocurrency: Withdrawals are fast, often completed within a few hours. Security Measures F8BET prioritizes player safety: SSL Encryption: Protects all financial and personal data. Verified Transactions: Each deposit and withdrawal is monitored for security. Trusted Payment Partners: F8BET works with reputable financial providers. Tips for Smooth Transactions Verify Your Account: Complete KYC (Know Your Customer) to avoid delays. Check Minimums and Maximums: Each payment method has specific limits. Use the Same Method for Deposit and Withdrawal: Ensures faster processing. Monitor Your Bank Statements: Keep track of transactions to avoid errors. Contact Support if Needed: F8BET customer service is available 24/7 for banking issues. Mobile Banking Convenience F8BET’s mobile platform supports all deposit and withdrawal methods. Manage your funds directly from your smartphone or tablet. Mobile banking maintains the same security and speed as desktop transactions. Conclusion Safe and fast banking is a key part of an enjoyable online casino experience, and F8BET excels in this area. With multiple deposit and withdrawal options, advanced security measures, and efficient processing, players can focus on slots, table games, and live casino action without worrying about payments. By following simple tips like account verification, tracking transactions, and using consistent payment methods, you can enjoy a smooth banking experience every time. Deposit, play, and withdraw with confidence at F8BET—your secure online casino destination!

1 0

confirm
by 汪洋 05 Nov '25

05 Nov '25

 confirm c28d09cf0893ee23fc780e120106b9b266ea0623

1 0

ChimeraX VR (specifically LookSee)
by jrj.healey＠gmail.com 02 Nov '25

02 Nov '25

Hi all, I'm trying to get ChimeraX VR standalone working on a Quest 3. Trying to follow the instruction online, but I fall at pretty much the first hurdle trying to subscribe to the release candidate channel on Meta AppLab - I get an error saying the channel is out of date or can no longer be found (or something to that effect). Do you have any more information on this, and does this mean side-loading is my only option potentially? Thanks Joe

3 2

What is the University of Michigan manufacturing partnership with LS Manufacturing?
by altabunny9_at_gmail.com＠mail.d2l.msu.edu 01 Nov '25

01 Nov '25

In today’s rapidly evolving industrial landscape, the manufacturing sector stands at the intersection of innovation and technology. From 3D printing (additive manufacturing) to CNC machining (subtractive manufacturing), modern engineers are required to bridge the gap between theory and real-world application. Recognizing this growing need, the University of Michigan’s College of Engineering has established a ground-breaking partnership with LS Manufacturing, a leading global on-demand manufacturing company. This collaboration—centred around the University of Michigan manufacturing partnership initiative—aims to provide students with hands-on experience in additive and subtractive manufacturing education, bridging academic theory with real-world industrial practices. Together, they are shaping the next generation of manufacturing engineers, innovators, and entrepreneurs. <ol> <li>Introduction</li> </ol> Manufacturing today is not just about producing parts; it’s about producing ideas, efficiency, and sustainability. The rise of additive manufacturing technologies such as 3D printing, alongside traditional subtractive manufacturing methods like CNC machining, has transformed how engineers design, test, and create. Yet, one challenge remains constant in academia—how can students gain real-world manufacturing experience before entering the workforce? Hands-on education is crucial to understanding how concepts like material tolerances, design for manufacturability (DFM), and prototyping translate from theory into production. To address this, the University of Michigan Engineering Department, in partnership with LS Manufacturing, launched a forward-thinking initiative to blend classroom learning with industrial collaboration. This partnership emphasizes rapid prototyping for academic research, student project sponsorship in CNC machining, and opportunities for real-world manufacturing experience for students through capstone project sponsorships and innovation-focused technical grants. <ol start="2"> <li>The Partnership’s Vision & Goals</li> </ol> The University of Michigan manufacturing partnership with LS Manufacturing was born from a shared vision: to cultivate a new generation of engineers fluent in both the digital and physical realms of production. Goal 1: Enhance Student Learning At its core, the partnership focuses on improving how students learn and apply manufacturing principles. By providing access to industrial-grade manufacturing equipment, students can design, prototype, and refine projects using professional tools like high-precision CNC machines and advanced 3D printers. This approach transforms the University of Michigan’s classrooms and labs into dynamic, industry-connected learning environments. Students don’t just learn about manufacturing—they experience it firsthand. Goal 2: Bridge Theory and Practice Engineering theory provides the foundation for design, but practice makes it meaningful. Through this partnership, students engage directly with industry partners from University of Michigan Engineering and LS Manufacturing experts. They receive practical insights into design for manufacturability (DFM), rapid prototyping, and low-volume production—critical skills that align with modern industry expectations. For instance, when developing prototypes, students can leverage rapid prototyping for academic research, gaining experience in both additive and subtractive processes. This real-world engagement ensures they are not only technically proficient but also ready to innovate efficiently. Goal 3: Foster Innovation Innovation thrives at the intersection of creativity and capability. The University of Michigan partnership supports student-led initiatives such as the Solar Car Team, Robotics Club, and Formula SAE by providing manufacturing expertise, technical feedback, and production services. From concept sketches to final assembly, LS Manufacturing’s involvement helps these teams iterate faster and smarter. This collaboration empowers students to push the boundaries of engineering innovation while gaining the confidence to lead future industry breakthroughs. <ol start="3"> <li>How the Partnership Works: The “LS Manufacturing Technical Grant”</li> </ol> At the heart of this collaboration lies the LS Manufacturing Technical Grant, a unique sponsorship-in-kind program designed to empower student innovation. Through this grant, LS Manufacturing offers selected University of Michigan student projects and faculty research initiatives a combination of expert DFM feedback, rapid prototyping services, and production support using state-of-the-art CNC machining, 3D printing, and injection molding technologies. This model represents a corporate sponsorship in manufacturing that prioritizes educational value and accessibility. Rather than a traditional cash grant, it provides students with tangible, high-impact resources—professional-grade components, real-time consultation, and access to global production networks. Application Process The process is simple and inclusive. Student teams, faculty members, or research labs can apply through the University of Michigan Engineering Department’s partnership portal. Applicants outline their project goals, design needs, and desired manufacturing processes. Selected participants receive LS Manufacturing’s technical support to bring their designs to life. This initiative promotes student project sponsorship in CNC machining and similar technologies, encouraging students to prototype and test ideas efficiently. It’s a hands-on, learning-by-doing opportunity that merges academic ambition with industrial capability. <ol start="4"> <li>Expected Impact & Benefits for UM Students</li> </ol> The collaboration’s impact extends far beyond the classroom. It delivers a transformative learning experience by combining advanced technology, mentorship, and real-world exposure. Access to Global Manufacturing Networks Through LS Manufacturing’s online instant quoting platform, students gain access to a vast global manufacturing network. They can upload designs, receive cost estimates instantly, and understand how design choices affect pricing and feasibility. This mirrors real-world industry practices, preparing them for professional engineering roles where digital manufacturing tools are essential. Reduced Project Costs and Lead Times Student projects often face challenges such as limited funding and long turnaround times. LS Manufacturing helps address both issues by providing cost-effective production support and faster lead times. Whether it’s producing a prototype for a capstone project or components for research testing, students can move from concept to prototype at record speed. Skill Development and Industry Interaction Beyond technical proficiency, this partnership develops professional skills—teamwork, communication, and project management. Students interact directly with LS Manufacturing’s engineering experts, gaining feedback on design feasibility and manufacturing optimization. Such exposure provides a window into real-world manufacturing experience, helping them bridge the often-cited gap between academia and industry. Accelerated Research and Innovation For faculty and graduate researchers, access to LS Manufacturing’s rapid prototyping services means faster testing and iteration cycles. Projects that once took months to prototype can now progress in weeks, enabling researchers to focus more on innovation and less on logistical barriers. Ultimately, this partnership enhances not just student outcomes, but the entire research ecosystem at the University of Michigan. <ol start="5"> <li>About LS Manufacturing</li> </ol> LS Manufacturing is a global leader in on-demand manufacturing and rapid prototyping services, empowering innovators and engineers to move from prototype to production with speed and precision. Their core capabilities include CNC machining, 3D printing, injection molding, and sheet metal fabrication—making them a one-stop solution for any stage of the manufacturing process. Through collaborations with academic institutions, LS Manufacturing demonstrates its commitment to supporting education, innovation, and workforce development. By working with the University of Michigan, the company is investing in the future of engineering talent and helping shape the next generation of manufacturing leaders. To learn more about their services and mission, visit <a class="external" href="http://www.lsrpf.com" target="_blank" rel="noreferrer noopener">www.lsrpf.com</a>. <ol start="6"> <li>Conclusion & Looking Ahead</li> </ol> The partnership between the University of Michigan and LS Manufacturing exemplifies what’s possible when academia and industry work hand in hand. By merging additive and subtractive manufacturing education with real-world applications, the collaboration equips students with the tools, experience, and confidence to lead the future of manufacturing. Through the LS Manufacturing Technical Grant, University of Michigan students are not only designing innovative products but also learning how to manufacture them efficiently—a skill set that’s indispensable in the global economy. As this partnership continues to grow, it promises to inspire new research collaborations, support entrepreneurial initiatives, and redefine how engineering education meets the demands of modern manufacturing. The future of the industry depends on creative thinkers, hands-on problem solvers, and innovators—and this program ensures they’re ready to lead. <ol start="7"> <li>Call to Action (For the UM Audience)</li> </ol> Faculty and student teams interested in exploring manufacturing innovation or applying for the LS Manufacturing Technical Grant are encouraged to contact the University of Michigan College of Engineering Department of Mechanical Engineering or visit the UM Engineering Partnership Page for more information. This is more than a sponsorship—it’s a movement toward redefining how students learn, design, and build. Together, the University of Michigan and LS Manufacturing are crafting the future of engineering education—one prototype at a time. FAQs <ol> <li>What is the University of Michigan manufacturing partnership with LS Manufacturing?</li> </ol> The University of Michigan manufacturing partnership with LS Manufacturing is a collaborative program designed to give students hands-on experience in modern manufacturing technologies. It combines additive (3D printing) and subtractive (CNC machining) education, helping students bridge the gap between classroom learning and real-world industrial practice. <ol start="2"> <li>How does the LS Manufacturing Technical Grant benefit University of Michigan students?</li> </ol> The LS Manufacturing Technical Grant provides selected students and faculty projects with in-kind sponsorship. This includes DFM (Design for Manufacturability) feedback, rapid prototyping services, and production support using advanced manufacturing technologies. It reduces project costs, shortens lead times, and gives students direct access to industry-level expertise. <ol start="3"> <li>Who can apply for the LS Manufacturing Technical Grant at the University of Michigan?</li> </ol> The grant is open to University of Michigan students, faculty members, and research teams involved in academic or innovation-based projects. Applications can be submitted through the University of Michigan Engineering Department’s partnership portal, detailing project goals and manufacturing requirements. <ol start="4"> <li>What kind of real-world experience do students gain through this partnership?</li> </ol> Students gain real-world manufacturing experience by collaborating directly with LS Manufacturing engineers, learning about design for manufacturability, rapid prototyping, and low-volume production. They also gain exposure to digital tools like instant quoting platforms and online manufacturing networks, preparing them for careers in modern industry. <ol start="5"> <li>How can faculty or student teams learn more about the LS Manufacturing partnership?</li> </ol> Interested participants can visit the University of Michigan College of Engineering’s Partnership Page or contact the department directly for detailed program information. The page includes application guidelines, eligibility details, and examples of past capstone project sponsorships supported by LS Manufacturing.

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Further help
by Emily Cioppa 29 Oct '25

29 Oct '25

Good evening, In addition to my previous question, I am also having difficulty appending chains. If I import molecular models into Chimera/ChimeraX that each have individual model names and singular Chain IDs, is there a way to combine these into a singular model and renumber the residues as one continuous sequence throughout the combined model? For example, I have three molecular models that are each components of a single RNA molecule, and each have their own pdb file and a singular Chain ID. I know how to physically orient all of them spatially and renumber the residues of each such that when hovering over the molecular model moving from 5’ to 3’ the sequence numbering is continuous and correct across all chains. However, even when I combine the three individual models into one at the beginning and change the chain IDs of all three to be the same ID at the end, when I view the combination model in sequence viewer, it has just appended all three chains together with no regard to residue order. Since each of the three models is a chunk of double helix, I would need the numbering to be in 5’ to 3’ order throughout the entire combination model sequence viewer, in the way that I have renumbered it and in the way that it is in the visible combined model/structure. Thank you for your help.

2 1

Help with Chain ID commands
by Emily Cioppa 29 Oct '25

29 Oct '25

Good evening, I have a quick question regarding the changechains command in Chimera/ChimeraX. If I have a single model open that inherently has one single chain, is there a way to select a continuous strand of residues in the sequence and change the Chain ID of only the selected residues to something else? It seemed from my online research that this is possible, however, I cannot get it to work. Any advice would be appreciated as soon as possible. Thank you. Best, Emily Cioppa Research Assistant The Rockefeller University

2 1

Average attribute
by Reza Khayat 29 Oct '25

29 Oct '25

Hi, How do I average atom attributes to residue attributes? Let's assume the attributes name is mapvalues. Thanks. Best wishes, Reza Reza Khayat, PhD City College of New York Department of Chemistry and Biochemistry

3 3

Align x,y,z axis of Proteins
by Hübbers, Jan 29 Oct '25

29 Oct '25

Hey support, I have defined x, y, z symmetry axis for a protein complex by forcing axis through centroids of the different subunits. I also created x, y ,z axis that meet at the origin of my scene. Is it possible to align the protein axis to the scene axis? Best, Jan ________________________________________________________________ Dr. rer. nat. Jan W. Hübbers Postdoctoral researcher RWTH Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology Assistant Features Editor The Plant Cell, American Society of Plant Biologists Worringerweg 1, 52074 Aachen, Germany +49 (0)241 80 28130 http://www.bio1.rwth-aachen.de/PlantMolCellBiology/index.html<https://urldefense.com/v3/__http:/www.bio1.rwth-aachen.de/PlantMolCellBiolo…> “The greatest value of a picture is when it forces us to notice what we never expected to see.” John W. Tukey

3 3

ChimeraX pre-built tar package
by Elaine Meng 28 Oct '25

28 Oct '25

> On Oct 22, 2025, at 3:57 PM, Charitha Belluru Shetty via Chimera <chimera(a)cgl.ucsf.edu> wrote: > > Hi Team, > We have the license for ChimeraX in name of Jim Thorpe. Would it be possible to provide the pre-built tar package of the latest version for Redhat 9. > With the previous version we were able to download the pre-build tar package from your website (example: ChimeraX-0.93.tar.gz), but now I see there is only .rpm package (https://www.rbvi.ucsf.edu/chimerax/download.html ) which will need to be installed in the OS level. I was looking to get a pre-build tar file for the latest version so we can install it without having to do the rpm install. I am aware there is github source for ChimeraX where we can build but would greatly appreciate if you could provide tar installer. Thank you! > $ cat /etc/redhat-release > Red Hat Enterprise Linux release 9.4 (Plow) > Best Regards, > Charitha Shetty Hello Charitha Shetty, ChimeraX usage & support questions should be sent to chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (without any data that should be kept private) since the commercial licensing team cannot answer that type of thing. I've CCd that address so you don't need to send your question again. I don't see that as an option on our download page, so my guess is probably not, but we can see if others on the list respond. Regards, 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

4 4

Problems with script
by George Tzotzos 28 Oct '25

28 Oct '25

I’d be grateful for your help My script is: # Auto-generated by make_chimerax_assets.py # Visualize L1 composition divergence on delta (1PN9) and epsilon (2IMI) open viz/delta_1PN9.pdb open viz/epsilon_2IMI.pdb defattr viz/delta_div.defattr model #1 defattr viz/epsilon_div.defattr model #2 style #1,#2 cartoon cartoon smoothRibbon true color byattribute divergence palette bluesred range 0,1 #1 color byattribute divergence palette bluesred range 0,1 #2 key colorbar palette bluesred range 0,1 label "Δ composition (L1)" pos 0.85,0.15 size 0.03,0.5 lighting soft zoom true When I try to open the color_delta_epsilon_divergence.cxs (see above), I get: RuntimeError: Not a ChimeraX session file File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 798, in restore raise RuntimeError("Not a ChimeraX session file”) Thank you

3 5

MCP for ChimeraX
by Alexis Rohou 27 Oct '25

27 Oct '25

Hi all, I would like to use ChimeraX via an agent. Quick googling suggests I'm not the first person to think of this (here <https://github.com/chatmol/molecule-mcp>, here <https://github.com/GDAmitha/chimerax-alphafold-mcp>), but before I dive in I thought I'd check - anyone else actively working on this? Or maybe you have worked on it and hit a roadblock? Cheers, Alexis

6 14

Problem with Boltz-2
by Dr. Oscar Perez 23 Oct '25

23 Oct '25

Hello ChimeraX Support, I am trying to use Boltz within ChimeraX to analyze ligand binding affinity, but I cannot find the corresponding option. I do not see any menu item or text that says “Predict Binding Affinity for.” [cid:51284bde-0c95-4cd2-bdd4-9570eef8bf69] When I run an example similar to the one shown in your video for the HIV protease<https://www.youtube.com/watch?v=h06yOBcaOqc> to evaluate ligand interactions, I obtain the generated 3D structure, but no table with ligand prediction values is produced. I installed ChimeraX just yesterday, so I assume I am using the latest version. Boltz is installed inside ChimeraX as well. Could you please advise how I can obtain the ligand interaction values? Thank you, Oscar Oscar Perez-Leal, MD Associate Professor Moulder Center For Drug Discovery Research Temple University School of Pharmacy 3307 N Broad St, Room 556 Philadelphia, PA, 19140 Tel: 215-707-4871 [cid:e222d198-ed2f-42a9-91a3-dab997f1387c]<https://outlook.office.com/bookwithme/user/3647ce5c96e849969435512aaf86933a…> Book time to meet with me<https://outlook.office.com/bookwithme/user/3647ce5c96e849969435512aaf86933a…>

2 1

Question about density map visualization for figures using ChimeraX
by Abhipsa Shatarupa 23 Oct '25

23 Oct '25

Hello, I am currently preparing figures for a publication and am using ChimeraX to render a density map. The color of the mesh representation I am using is set to *licorice*, but after I save the image in TIFF/PNG format at 7602 × 5680 resolution, the mesh appears quite faint. Could you please advise on how to make the density appear darker or more prominent in the saved image? Thank you! -Abhipsa

4 3

Building ions using ISOLDE
by Przemyslaw Dutka 22 Oct '25

22 Oct '25

Hello, I am currently encountering an issue while trying to build Na ions with ISOLDE. Despite various attempts, the ions consistently move outside the density as soon as the simulation begins. The ion site is clearly defined by previous crystallography maps. I have also downloaded several EM maps that include modeled Na ions, such as PDB 6VWX (see below). In these cases, the ion still moves up or down the channel once the simulation starts. The only method I've found to keep the ion in place is by pinning it. I would greatly appreciate any advice or tips. [image: Screenshot 2025-10-21 at 10.33.05 PM.png] Best, Przemek

2 1

building on macOS
by Alexis Rohou 21 Oct '25

21 Oct '25

Hello, I'd like to build from source in order to play with (and possibly hack at) the MCP server. I am on macOS 14.7.6 with Xcode 16.2. I think the compilation went well, but at link time I get warnings and an error. Below is the end of the output of `make install`. What do you recommend I try? Cheers, Alexis available bundle cache has not been initialized yet Executing: devel install . user false exit true noDeps true ld: warning: object file (/Users/rohoua/work/git/ChimeraX/src/bundles/atomic_lib/atomic_cpp/pyinstance_cpp/PythonInstance.o) was built for newer 'macOS' version (11.0) than being linked (10.9) ld: warning: object file (/Users/rohoua/work/git/ChimeraX/src/bundles/atomic_lib/atomic_cpp/element_cpp/Element.o) was built for newer 'macOS' version (11.0) than being linked (10.9) ar: src/lib/libatomstruct_tmpl.a is a fat file (use libtool(1) or lipo(1) and ar(1) on it) ar: src/lib/libatomstruct_tmpl.a: Inappropriate file type or format Traceback (most recent call last): File "/Users/rohoua/work/git/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/_distutils/spawn.py", line 87, in spawn subprocess.check_call(cmd, env=_inject_macos_ver(env)) File "/Users/rohoua/work/git/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py", line 413, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/usr/bin/xcrun', 'ar', 'rcs', 'src/lib/libatomstruct_tmpl.a', 'atomic_cpp/atomstruct_cpp/tmpl/Atom.o', 'atomic_cpp/atomstruct_cpp/tmpl/Bond.o', 'atomic_cpp/atomstruct_cpp/tmpl/CoordSet.o', 'atomic_cpp/atomstruct_cpp/tmpl/Molecule.o', 'atomic_cpp/atomstruct_cpp/tmpl/Residue.o', 'atomic_cpp/atomstruct_cpp/tmpl/TemplateCache.o', 'atomic_cpp/atomstruct_cpp/tmpl/amino.o', 'atomic_cpp/atomstruct_cpp/tmpl/camino.o', 'atomic_cpp/atomstruct_cpp/tmpl/findres.o', 'atomic_cpp/atomstruct_cpp/tmpl/general.o', 'atomic_cpp/atomstruct_cpp/tmpl/ions.o', 'atomic_cpp/atomstruct_cpp/tmpl/namino.o', 'atomic_cpp/atomstruct_cpp/tmpl/nucleic.o']' returned non-zero exit status 1.

2 3

questions for ChimeraX
by Jéromine Carret 21 Oct '25

21 Oct '25

Hello, My name is Jéromine, and I am a PhD student at the University of Lille, France. We are working on structural modelling of different protein variants. We have questions about the ChimeraX software tools. We would like to obtain electrostatic maps of protein structures and avoid using the colour scale in order to obtain numerical results. And also for hydrophobicity maps. We also want to study the clashes between the positions of variants. Do you have any advice? For the matchmaker command, can you give me the information I need to understand the results? Thank you in advance for your reply. Kind regards. Jéromine Carret PhD candidate RADEME lab ULR 7364 Université de Lille

2 3

chimeraX daily built, 2025 Oct 20, boltz-2 empty sequence line in yaml file
by Guenter Fritz 20 Oct '25

20 Oct '25

Dear ChimeraX developers, really a great job implementing boltz into chimeraX !! I have just installed the latest daily build 2025 Oct 20 on a Redhat 8 (Rocky 8 derivative) machine. Boltz-2 installs with no visible problem via chimeraX (like before). When I try to run predictions, I get an error which seems to be due to an almost empty yaml file created by chimeraX. Only the first line ("version 1.0") is in the yaml file. Boltz (of course) fails. There should be no problem with permissions. I just installed also the latest release of chimeraX and boltz-1 via chimeraX. Runs as expected. PS: I had no try yet on my mac (will check later). Best wishes, Guenter

2 3

Problems adjusting the phi/psi angles with ChimeraX
by Gong, Zhen 15 Oct '25

15 Oct '25

Dear ChimeraX team, I was trying to use ChimeraX to change the phi/psi angles of a residue in the loop region but encoured this error: ILE 411 N ↔ CA is part of a ring/cycle and cannot be rotated. There is no ring/cycle in ILE411 or neibouring residues: ASN 410 or THR 412. I tried ChimeraX daily (version 1.10.dev202504260127 (2025-04-26) and ChimeraX 1.10.1 but the same error happened. I am wondering if it is possible to change the phi/psi angles with ChimeraX. Thank you. Best, Zhen

2 3

Chimera and ChimerX issues after update to MacOS Tahoe
by Rechiche, Othman 14 Oct '25

14 Oct '25

Hi everyone, I recently updated to MacOS Tahoe, Since then I encountered several issues with Chimera, ChmieraX and python. I installed and removed and reinstalled the apps but I still get the same error. For chimera I get this error: [Screenshot 2025-09-24 at 12.08.51 AM.png] FOr ChimeraX, when I try to open a session, it complains that the session was created with another version of python. I opened that session successfully several times before to the update of MacOS and I have never seen this error before. Failed opening file /Users/x/x/x/x/x/x/x/x.pyc: Python code was compiled for a different version of Python Can you please help me fix this? Best Regards, Othman Dr. Othman Rechiche Herbert Irving Comprehensive Cancer Center Columbia University Medical Center Columbia University New York, NY 10032 email: or2296(a)cumc.columbia.edu phone: +1 (814) 880-5554

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help on color command
by James Raymond 12 Oct '25

12 Oct '25

Dear ChimeraX, I have tried 100 variations of color command without success. Can you tell me the command to color residues 132-145 red in this single chain protein? thank you Jim [image: image.png]

2 1

Issue with combining two pdb models in chimeraX
by Rayees Mattoo 10 Oct '25

10 Oct '25

Hi, I have two models #1 Model1.pdb and #2 Model2.pdb having one shared polypeptide, same chain ID but different residue numbers. I wanted to combine them to make a merged_model #3. I used the following combine commandline in chimeraX: combine #1 #2 close false modelId #3 retainIds true name merged_model The resulting combined model appeared to be correct, and I proceeded to run phenix.real_space_refine without any issues. However, when I attempted to deposit the refined model (either in .pdb or .cif format) with the wwPDB, I received a file with multiple errors (see attached). Interestingly, I had previously deposited the individual models (#1 and #2) without any problems. This situation raises my concern about whether the combination process was successful. Is there anything I should have done differently to ensure a seamless combination of the models? Best Rayees

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ChimeraX-1.10.1 syntax issue
by wwvivian.wang＠mail.utoronto.ca 10 Oct '25

10 Oct '25

Hi, this is my first time using ChimeraX-1.10.1 and I ran into a little bit of trouble with syntax errors in this version.\ I opened a pdb file that contains two chains of proteins that I'm interested in - Chain A and B. I then renamed and coloured them to Chain C and D for clarity. In the Contacts window, I made the following changes: Find pairs of atoms with: ✅ VDW overlap ≥ –0.4 Å Limit by selection: ✅ with at least one end selected Ignore interactions between atoms 4 or fewer bonds apart: ✅ Ignore interactions between residues <5 apart: ✅ Include intermodel: ✅ Include intramodel: ❌ (uncheck it) Include intramolecule: ❌ (uncheck it) Ignore hidden models: ✅ Display as pseudobonds: ✅ (keep green, radius 0.075, dashes 6) Write info to: Log ✅ Then click Apply I then selected the atomic model #1 (Chain C+D) and deselected surface models #1.1 (Chain C) and #1.2 (Chain D) and ran the Contacts Command: "contacts atoms #1/C #1/D makePseudobonds true distanceCutoff 4.0 log true" but the software returns "Expected a keyword" argument and highlighted "distanceCutoff 4.0 log true" in red. Alternatively, I also tried "findclash #1/C test #1/D overlapCutoff -0.4 hbondAllowance 0 interModel true intraMol false intraRes false makePseudobonds true select true log true" but again it fails to output contact coordinates between the two chains and returns the following: "Unknown command: findclash #1/C test #1/D overlapCutoff -0.4 hbondAllowance 0 interModel true intraMol false intraRes false makePseudobonds true select true log true". I would appreciate your help in resolving this error for me. Thanks, Vivian

2 1

Focus in ChimeraX
by Luca Pellegrini 10 Oct '25

10 Oct '25

Hi, What is the ChimeraX equivalent to the Focus command in Chimera? I have selected a portion of a structure, and would like to bring it into focus without dragging it into view. Also Focus would automatically set the selection as the pivot point. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA lp212(a)cam.ac.uk

4 3

Question about using ChimeraX
by 张圃源 09 Oct '25

09 Oct '25

Hi， I'm a new user of ChimeraX and I'm currently facing a problem. I want to convert a pdb file into an mrc file that can be input into cryoSPARC, and this mrc file should be in the form of a cube volume. I will use ChimeraX to achieve this. How should I proceed? Best Yuan 中山大学张圃源

2 1

tools for ligand-receptor interactions
by Elaine Meng 09 Oct '25

09 Oct '25

> On Oct 8, 2025, at 9:58 AM, Vojo P Deretic <VDeretic(a)salud.unm.edu> wrote: > > Hi > How do I pose a question - via email or on the site? > My question is: we have a Boltz/alphafold fitted organic molecule into a known structure. > What are the tools for residue interactions in ChimeraX apart from H bonding and hydrophobic or charged surfaces? > Thanks > Vojo Deretic > Hi Vojo, As per the Contact Us page <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html> ...to ask questions you would use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address, which is CC'd here so you don't need to send your questions again. I don't know what you mean by "on the site" since there is no webform for questions, only this email address. You already mentioned H-Bonds and coloring the receptor molecular surface by ESP (electrostatics) or MLP (lipophilicity). That's most of it. Certainly you can just visually evaluate what is nearby, but you could use the Contacts tool for a more objective approach: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> See also the tutorial "Protein-Ligand Binding Sites" <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.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 Oct 8, 2025, at 9:58 AM, Vojo P Deretic <VDeretic(a)salud.unm.edu> wrote: > > Hi > How do I pose a question - via email or on the site? > My question is: we have a Boltz/alphafold fitted organic molecule into a known structure. > What are the tools for residue interactions in ChimeraX apart from H bonding and hydrophobic or charged surfaces? > Thanks > Vojo Deretic > > Sent from my iPhone with lots of typos and autocorrect nonsense - my apologies... >

2 5

Append ligand coordinates from one PDB to another
by George Tzotzos 08 Oct '25

08 Oct '25

I’m dealing with two structurally similar proteins, one of which is in complex with a ligand (pdb1). The second protein is in the apo-form (pdb2). I’ve used matchmaker to superimpose the structures. Does it make sense to append the ligand coordinates to pdb2? I’m interested to find out which residues lie within 4-5 Å from the ligand. Probably a better approach would be to dock the ligand to pdb2. Could this be done through ChimeraX using Boltz2? Thank you for your suggestions. George

2 2

Issue in displaying pdb in chimeraX
by Rayees Mattoo 07 Oct '25

07 Oct '25

Hi, I merged two molecules in coot and generated a merged.pdb file. However, upon displaying in ChimeraX part of my model is cartoon and part of it displays as worm, see the attachment. After running dssp I can fix it, but I want it to display as cartoon by default. Anything I need to edit in the merged.pdb file? Best Rayees

2 1

Modeller interface
by Alexandra Zahradnikova 07 Oct '25

07 Oct '25

Hi All, Today I am getting problems when trying to model loops with Modeller. Repeatedly (on different structures), the following error occurs: modeller refine 1/A:1:internal-missing numModels 1 fast false adjacentFlexible 1 protocol standardException in thread Thread-33 (_run_function): Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.10\bin\Lib\threading.py", line 1038, in _bootstrap_inner self.run() File "C:\Program Files\ChimeraX 1.10\bin\Lib\threading.py", line 975, in run self._target(*self._args, **self._kwargs) File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-packages\chimerax\core\tasks.py", line 300, in _run_function func(*args, **kw) File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-packages\chimerax\webservices\cxservices_job.py", line 156, in run reason = json.loads(e.body)["description"] ^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10\bin\Lib\json\__init__.py", line 346, in loads return _default_decoder.decode(s) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10\bin\Lib\json\decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10\bin\Lib\json\decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0). Is it a problem with the Modeler server? How can I find out in the future whether there is a problem with the server or the problem is in my input structure? Thanks in advance. Best regards Sasha

2 2

Re: [Chimera] local resolution map colors
by Elaine Meng 06 Oct '25

06 Oct '25

I can't tell anything from the image, since I have no idea what your filenames mean. All I can say (again) is you have to open both the original map and the local resolution map, show the original map as a surface, and use the local resolution map values to color that surface. Elaine > On Oct 3, 2025, at 2:32 PM, Roy Chowdhury, Shatabdi <Shatabdi.RoyChowdhury(a)ucsf.edu> wrote: > > Hi Elaine, > > Thanks for your reply. Attaching the new screenshot here. This shows that the map values are 0.1095 all over. Please let me know if I can give any additional information. > ~Shatabdi > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Friday, October 3, 2025 2:20 PM > To: Roy Chowdhury, Shatabdi <Shatabdi.RoyChowdhury(a)ucsf.edu> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera] local resolution map colors > !-------------------------------------------------------------------| > This Message Is From an External Sender > This message came from outside your organization. > |-------------------------------------------------------------------! > > 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 > > > <Screenshot from 2025-10-03 13-56-32.png><Screenshot from 2025-10-03 13-56-51.png>> _______________________________________________ > > Chimera mailing list -- chimera(a)cgl.ucsf.edu > > To unsubscribe send an email to chimera-leave(a)cgl.ucsf.edu > > > <Screenshot from 2025-10-03 14-29-30.png>

2 4

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

2 1

Struggling to complete assignment at last minute? Hire our Assignment helper
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04 Oct '25

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1 0

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

2 3

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

3 4

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

1 0

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

3 4

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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Is there a way to download a pdb and it's associated density map in one command
by Samuel Haysom 24 Sep '25

24 Sep '25

Is there any way I can fetch a pdb file from the web (e.g. $ open 1X2Y) and then also automatically fetch the associated cryoEM map if there is one? Looking in the mmCif file, there is a flag for the associated emdb-map (e.g. in 5ljo the mmCIF file there is a _pdbx_database_related.db_id flag with the corresponding id. It would be useful if this could be added as a flag to the open command if it isn't already. I'm sure it is also possible in some kind of script but I'm not hugely familiar with how to script in chimeraX. Samuel Haysom Senior Scientist • Protein Sciences Nxera Pharma UK Limited +44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

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Ligand center
by NUR AIDA SAKINAH 24 Sep '25

24 Sep '25

Hi ChimeraX teams, I want to search ligand center for docking analysis. What command do I need to use to retrieve the ligand center (x,y,z)? Example pdbid is 4yvv and the ligand is GBM. So i want the GBM's x,y,z coordinates. Thank you. Regards, Aida.

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Regarding the method used by chimeraX for SASA calculation
by Prathvi Singh 23 Sep '25

23 Sep '25

Hi Elaine, I have used NACCESS ( https://www.bioinf.manchester.ac.uk/naccess/nac_intro.html) to calculate the SASA for a protein. It used the Lee & Richards (1971, J. Mol. Biol., 55, 379-400) method to calculate SASA. I wanted to know whether chimeraX also uses the same method to calculate SASA or not. If not, then can you mention how the chimeraX method differs from the method used by NACCESS? Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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

23 Sep '25

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

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

19 Sep '25

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

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

18 Sep '25

Hello, I am trying to do something seemingly simple, but can't figure out what I am doing wrong. I have an mrc map open as model #1, moved the center of rotation somewhere, then generated a sphere with: shape sphere radius 30 center cofr I got a sphere as model #2, good. Then I want to turn this sphere into a mask, which I try doing like this: volume onemask #2 ongrid #1 At which point I get this error: Expected a density maps specifier or a keyword The documentation of 'volume onemask' says it needs a surface specification as the first argument, and the model panel shows that there is no surface associated to the sphere (then why/how is it displayed? not sure), so that all seems to make sense. And I am stuck at this step: how do I turn this sphere into a surface so I can generate a volume from it? I read the documentation for 'surface', 'volume' and 'shape' but can't find anything to solve this problem. Thank you in advance, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Guidance on SASA/RSA calculation in ChimeraX
by Kazi Sayeeda 16 Sep '25

16 Sep '25

Dear ChimeraX Support Team, I am currently using ChimeraX (v1.10.1) to study whether certain amino acid residues are surface-exposed or buried in my protein structures (WT and mutants from AlphaFold/NeuroSnap). To assess this, I measured solvent accessible surface area (SASA) with the following commands: measure sasa #1 measure sasa #1:92 measure sasa #1:562 This gives me the following SASA values (in Å²): * WT Ala92: 216.4 Å² * WT Gly562: 189.0 Å² When I compare these to published maximum ASA (MaxASA) values from Tien et al. 2013 (probe radius 1.4 Å): * Ala (max ASA) = 129 Å² * Gly (max ASA) = 104 Å² I get relative solvent accessibility (RSA) values greater than 1: * Ala92: 216.4 / 129 = 1.68 * Gly562: 189.0 / 104 = 1.82 Since RSA should not exceed 1, I believe I am mismatching ChimeraX’s calculation settings with the MaxASA reference set. So my questions are: 1. What radii model and probe radius does measure sasa in ChimeraX use by default? 2. Is there a way in ChimeraX to directly assign per-residue SASA attributes and normalize them internally (so RSA values remain ≤1)? 3. If ChimeraX defaults differ from published MaxASA tables, would you recommend reporting only SASA values, or generating my own MaxASA reference values with ChimeraX for consistency? I would be very grateful for any guidance or documentation pointers so I can report values in a way that is consistent and interpretable. Best, Kazi Sayeeda PhD Candidate Dept. of Cell and Developmental Biology (Krendel Lab) SUNY Upstate Medical University Syracuse, NY 13210 sayeedak(a)upstate.edu<mailto:%20sayeedak@upstate.edu>

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Re: scan results for vr.ucsf.edu
by Tom Goddard 15 Sep '25

15 Sep '25

Hi Greg, The web site report for vr.ucsf.edu <http://vr.ucsf.edu/> you shared takes me to web site that requires a login if I want to see what links are broken. Tom > On Sep 15, 2025, at 6:04 PM, Siteimprove Reports <reports(a)siteimprove.com> wrote: > > > Hi there, > Greg Couch (gregc(a)cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>) wants to share a dashboard report with you. The report was generated from "DCI score dashboard" at 6:02 PM on 9/15/2025. > > View report <https://reports.siteimprove.com/sendnow/8343/c77e8c4c-b3d9-4ba5-b4eb-1c17a3…> > > > > > > > > > > View report <https://reports.siteimprove.com/sendnow/8343/c77e8c4c-b3d9-4ba5-b4eb-1c17a3…> > > © 2025 Siteimprove > Havneholmen 33, DK-1561 Copenhagen, Denmark >

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Display the bfactor value when the mouse goes over a residue?
by Vincent CHAPTAL 15 Sep '25

15 Sep '25

Hello, I'd like to know, in addition to residue name and model, the bfactor of a residue when the mouse goes over it. For example model#1.20/A PHE 1482 bfactor 120.7 Could you help me to do it? Thanks a lot. Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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