June 2026 - ChimeraX-users - RBVI Mailing Lists

ISOLDE 1.12 released
by Tristan Croll 26 Jun '26

26 Jun '26

Hi all, I'm happy to announce that ISOLDE 1.12 is now released, for use with ChimeraX 1.12. A few new developments: - courtesy of Alexis Rohou, new "isolde preflight", "isolde validate", "isolde status", "isolde add disulfides", "isolde clear altlocs" and "isolde load parameters" command sets. The first three are explicitly read-only: they make no changes to the model state - they just help check if the model is simulation-ready, report standard geometric validation stats, or the current simulation/no simulation status of ISOLDE itself. The remainder add command-line access to features that were previously GUI-only, bringing things more in line with ChimeraX standards. - one for the expert users (as a stepping-stone to better things later): you can now use the command "setattr {residue} isolde_template_name {template name}" to tell ISOLDE to skip automatic template assignment and apply the specified MD template for simulation purposes. Should be of particular use for those who are experimenting with covalent ligands. - in a similar vein, custom-user-loaded ffXML templates will now be respected for polymeric residues (previously, they could only be applied to ligands). Also, loading a template of the same name will now override the previous template rather than failing. - A few minor tweaks and bugfixes (mainly to the Ramachandran plot). Best, Tristan -- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT

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from .pdb to .stl conversion with pbonds
by Vincent CHAPTAL 25 Jun '26

25 Jun '26

Hi, a little off-topic question, but not completely... a standard conversion of .pdb to .stl works very well and 3D prints perfectly. I encounter a problem with the addition of pbonds as in the attached image. converting an atom in a sphere of larger diameter is fine (top image). But adding a pbond from the center of that sphere results in empty spaces created at the intersection between objects (bottom image, 2 white arrows). There is also no real cohesion between the 2 objects (left arrow), which results in a very weak printing. Any ideas on how to make the 2 object fuse entirely? Thank you. Vincent -- Vincent Chaptal, PhD CNRS research director Team leader Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 https://mmsb.cnrs.fr/en/team/drug-resistance-and-membrane-proteins-drmp/

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question about cartoon style strand xsection
by Vincent CHAPTAL 23 Jun '26

23 Jun '26

Hi, I want to modify the width of beta strands, so I use the command: car style strand xsection rect width 1 and it works very well. Now I want to modify only certain strands, so I use: car style strand xsection rect width 1 car style #2-10 strand xsection rect width 0.1 for the later command, I get the error "expected a keyword". But, when I use the same type of command for helices it works well: cartoon style #2-10 width 0.1 thick 0.1 Is there something I'm doing wrong in the script or it is not possible for strands? Thank you for your help. Vincent -- Vincent Chaptal, PhD CNRS research director Team leader Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 https://mmsb.cnrs.fr/en/team/drug-resistance-and-membrane-proteins-drmp/

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Isolde for ChimeraX 1.12 on Windows
by Christian Billesbølle 19 Jun '26

19 Jun '26

Hi, I am wondering if there is a scheduled update of ISOLDE to work with ChimeraX 1.12 on Windows? Thank you, Best regards / Med venlig hilsen ********************************************************** Christian Bache Billesbølle, PhD Principal Scientist Molecular Pharmacology phone: +45 53 75 42 86 cbillesboelle(a)zealandpharma.com<mailto:jmm@zealandpharma.com> [cid:image001.png@01DCFD97.17184DB0] Zealand Pharma A/S Sydmarken 11 2860 Søborg Denmark Tel: +45 88 77 36 00 Fax: +45 88 77 38 98 www.zealandpharma.com<http://www.zealandpharma.com/> This message, including attached files, may contain confidential information and is intended only for the use by the individual and/or the entity to which it is addressed. Any unauthorized use, dissemination of, forwarding, disclosure or copying of the information contained herein is not allowed and may lead to irreparable harm and damage for which you may be held liable. If you receive this message in error or if it is intended for someone else please notify the sender by returning this e-mail immediately and delete and destroy the original message and all copies.

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modeller comparative
by Roberto Marabini 18 Jun '26

18 Jun '26

Hi, I am using the ChimeraX modeller comparative command in both ChimeraX 1.7 and ChimeraX 1.11.1. The command executes successfully in both versions, but the results are significantly different. The model generated with ChimeraX 1.7 appears correct, whereas the model generated with ChimeraX 1.11.1 appears incorrect. One notable difference is the GA341 "correlation" score: it is close to 1.0 (high confidence) in ChimeraX 1.7, but close to 0.0 (very low confidence) in ChimeraX 1.11.1. The test data is: Sequence: UniProt P69905 (human hemoglobin) Template structure: PDB 2DHB (horse hemoglobin) Alignment: attached file The exact command used was generated using chimerax GUI: modeller comparative aligned_1.fasta:2 numModels 5 fast false multichain true hetPreserve false hydrogens false waterPreserve false Has anyone observed similar differences between ChimeraX versions, or can suggest a way to obtain consistent Modeller results in the latest releases of ChimeraX? Thanks in advance for any help. Roberto

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Exact meaning of RMSF (RMSD in sequence alignment)
by Alexandra Zahradnikova 17 Jun '26

17 Jun '26

Dear All, I was not able to find out what is the formula for calculating RMSF in the commans Sequences-> Headers-> Calpha. Does it calculate the RMSD per residue of distance between C-alpha of each of the associated sequence and the displayed sequence, or RMSD per residue between all of the associated sequences? Thank you very much in advance for explanation. Best regards Sasha

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ChimeraX 1.12 release
by Elaine Meng 12 Jun '26

12 Jun '26

UCSF ChimeraX version 1.12 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 1.11 (December 2025) include: - OpenFold3 structure prediction - Boltz server capabilities - cartoons with straight cylinder helices (alternative to curved tube helices) - 3D-SNFG glycan representations - Match->Align to create a multiple sequence alignment from a 3D superposition - label residues with color-coded grids of amino acid prevalences from an associated multiple sequence alignment in Profile Grid - Find Cavities options to include cofactors, restrict search to box - trajectory clustering - commands to reproduce clipping plane positions - Mutation Scores tool for analysis of deep mutational scanning results 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

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Re: nucleotide tube/slab or slab for modified nucleotides
by Daniel Larsson 11 Jun '26

11 Jun '26

A follow-up to the visualization of modified nucleotides as “slab”. The base of pseudouridine has the slab pointing in the wrong direction (probably due to the isomerization of the pyrimidine ring). This makes visualization of base pairs to PSU look wrong since the bases do not line up correctly (see attached image with PSU in purple in wrong position). Regards, Daniel From: Daniel Larsson via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Reply to: Daniel Larsson <daniel.larsson(a)icm.uu.se> Date: Wednesday, 13 May 2026 at 14:48 To: chimerax-users <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] Re: nucleotide tube/slab or slab for modified nucleotides Hi Elaine, Thank you for the quick feedback. My problem was that I was using PDB files without the proper mmCIF headers. ChatGPT was helpful in explaining that non-standard residues can have a designated parental compound, which is defined in the mmCIF header: loop_ _chem_comp.id _chem_comp.mon_nstd_parent_comp_id 2MA A 2MG G Since I had several PDB files where I had done refinement, alignments, scaling and other things, I did not want to go through the trouble of converting them all to mmCIF. But fortunately, it seems ChimeraX only keeps one definition of monomer non-standard parent compounds, so it was sufficient for me to load one proper .mmCIF downloaded from the PDB so get the mapping correct. Short story, I just ran “open 7k00 fromDatabase pdb format mmcif” and after that all my modified nucleotides rendered correctly. Regards, Daniel From: Elaine Meng <meng(a)cgl.ucsf.edu> Reply to: chimerax-users <chimerax-users(a)cgl.ucsf.edu> Date: Tuesday, 12 May 2026 at 17:32 To: Daniel Larsson <daniel.larsson(a)icm.uu.se> Cc: Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] nucleotide tube/slab or slab for modified nucleotides Hi Daniel, In my test of a recent daily build, 2MA and 2MG in PDB 7k00 are shown as slabs. Maybe you need a newer version of ChimeraX? ChatGPT should always suggest getting a recent version -- then it might have a higher success rate. 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. [cid:image001.png@01DCF82D.773F82E0] There was a ticket previously to show slabs for more modified bases (#1211) but closed 18 months ago. 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 > On May 12, 2026, at 6:59 AM, Daniel Larsson via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Is it possible to show modified nucleotides as tube/slab or slab? Some common modified residues are recognized as nucleotides, such as PSU, but not e.g. 2MA or 2MG (present in e.g. PDB 7K00)? ChatGPT suggested to rename the residues or redefine the polymer type, but these tricks do not work. > > 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 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. _______________________________________________ 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/

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UniProt ID detection and display from mmCIF files
by Samuel Nitz 10 Jun '26

10 Jun '26

Hello, I’m adding metadata to a large set of mmCIF files coming from a large-scale AlphaFold prediction effort. The goal is to have descriptions for each polypeptide chain visible when opening the file in ChimeraX. Adding descriptions is easy via the _entity.pdbx_description parameter. However, I can’t figure out how to add UniProt IDs so they show up in their own column, which is usually the case for files I’ve downloaded from the AlphaFold database or PDB. I’ve tried editing struct_ref and struct_ref_seq , but ChimeraX still won’t display the UniProt IDs. How do I do this? Version information: mmCIF dictionary: mmcif_ma.dic 1.4.5 ChimeraX: version 1.10 (2025-06-26) Thanks for your help! Sam Nitz PhD candidate, Rock lab Rockefeller University

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Changing Chain IDs in ChimeraX
by Parvate, Amar D 10 Jun '26

10 Jun '26

Hi My name is Amar and I am working on the structure of a phage tail complex. I have multiple dodecameric assemblies within the tail complex. Is there a way to change/name chain IDs from say P1 to P12 in chimeraX so that they are all read and rendered? Can I make ChimeraX read chains beyond P9 when I have numbered them from say P1 to P12? Coot reads it fine but ChimeraX gets confused after P9 (image attached). I cannot select chain "P12" or any residue/sidechain in it [cid:image001.png@01DCF8BD.9D7AF260] Best Amar

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