- ChimeraX-users - RBVI Mailing Lists

Question about minimization error with af3-produced protein–RNA complex in ChimeraX
by Bruno Hay Mele 09 Jul '26

09 Jul '26

Hi, I am trying to minimize an AF3-generated protein–RNA complex [1, attached] in ChimeraX [2,3] , but the minimization fails with the following error: `KeyError: 'RNA-o'` The traceback points to OpenMM while creating the system (`forcefield.createSystem()`). I assume AF3 uses standard nomenclature for atoms and residues, so I was wondering whether this is a known issue with the force field used by ChimeraX for minimization, or if there is a way to work around it. I am aware of the limitations of ChimeraX minimization and am only using it as a quick check before (eventually) proceeding with more rigorous refinement. Thank you for any suggestions. Best regards, -- Bruno Hay Mele, PhD https://github.com/bhym/ [1] metrics (pae/plddt/iptm) are very good [2] just plain minimize #1 [3] Daily build of couple days ago (UCSF ChimeraX version: 1.13.dev202607062345 (2026-07-06) )

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A question for GPI-anchored protein
by 落合廣 08 Jul '26

08 Jul '26

Dear DR. Thank you for using chimeraX. I am very impressed with the development of protein assembly analysis technology. I am an elderly (88-year-old) biochemist. 　I have a question. ○1. Even if dimer formation is analyzed by AlphaFold 3, dimers with interfaces are not recognized at all (AlphaFold has a list of 19(?) analyzed). Why? ○2. Even though dimer formation (54 or 132 interface residues) can be seen by chimeraX, when looking at ipTM with AlphaFold, a number such as 0.19 is not recognized as a dimer. Do you think that this is because AlphaFold does not take into account that proteins such as GPI membrane proteins are kept in anti-parallel, do you have an opinion? With best Regards Hiroshi Ochiai Research Institute for Electronic Sciences, Hokkaido University, Sapporo Japan Emeritus Professor

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Issues with rendering specific colors for nan values
by Jaewon Suk 07 Jul '26

07 Jul '26

Hello, I am sure this question is asked often, but I could not find a solution that solved my issues even with similar contexts. I am using a python script to prepare my .defattr files (.defattr file uploaded below). I have nan values that I would like to set as lightgray using ‘noValueColor light gray’ but to no avail. All nan values are locked in a dark gray/black color. I saw that there was a ‘finite range’ error with numpy, that might be occurring due to my first and last values being ‘nan’, but I still have the nan coloring issue when I manually assign my first and last values as 0.0. Other failed attempts to resolve this issue were: - setting my noValueColor to target residues ‘target r noValueColor light gray’ - setting all ‘nan’ values to blanks - manually rendering ’noValue’ to a specific color by Tool > StructureAnalysis > Render/ByAttribute. (The color in box is correct, but it does not render to the correct color. Thank you! Jaewon

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Simulations fail instantly ("Sim termination reason: None") across entire model, all fidelity levels, survives full restart + reinstall
by Guardado, John H. 06 Jul '26

06 Jul '26

Hi all, I'm running into a persistent issue in ISOLDE and would appreciate any guidance, especially from Tristan if he has a moment. ChimeraX version: 1.12 OS: Windows Summary: isolde sim start fails immediately with no simulation actually running, for essentially any selection in my model -- not just one problem region. The log shows: Sim termination reason: None ISOLDE: stopped sim with no further error detail, immediately after the residue templates (FAD, P6G, PO4) finish loading from the internal database. What I've ruled out so far: * Not a stuck/lingering Unparameterised Residue widget (confirmed via full ChimeraX restart) * Not specific to one problem residue -- originally isolated a specific residue (ASN, chain A) via bisection, but after fixing it (full atom+bond rebuild from a working homologous chain, confirmed via distance checks that backbone geometry was reasonable), the same failure then appeared in a completely unrelated, previously-working region of the model * Not a duplicate-atom/clash issue -- scanned for overlapping atoms (<0.6 A) in the affected region, found and removed a set of stray duplicate hydrogens, confirmed zero overlaps remaining; simulation still failed * Not an mmCIF metadata issue -- the same region on the model's other (homodimer) chain simulates without any problem * Not a session-state/cache artifact -- fails identically after closing ChimeraX entirely and reopening a freshly saved PDB from disk * Not a simulation fidelity/resource issue -- tested at Medium/Medium and Lowest/Fastest, identical failure both times * Not resolved by a full OS-level restart (not just closing ChimeraX) -- identical failure immediately after reboot, on a select /A:60-61 range that had previously worked earlier the same day * Not resolved by reinstalling the ISOLDE bundle via the ChimeraX Toolshed and restarting -- identical failure persists on previously-failing selections (/A:508-518, /A:60-86) immediately after reinstall; only the one range that had always worked (/A:60-61) "worked," which isn't diagnostic since it never failed in the first place Sequence that reproduces it (after a clean restart): open session_backup_03.cxs isolde start clipper associate #1.1.1.1 toModel #1.2 select /A:508-518 isolde sim start /A:508-518 Result: templates load (FAD/P6G/PO4), then immediate "Sim termination reason: None." The Problem Zones tab is empty, which I believe is expected since no simulation has ever successfully started to generate restraint data. Model contains a protein homodimer (two chains, otherwise identical) plus FAD, PO4, and P6G heteroatoms, refined via Servalcat from a cryo-EM map. Happy to share the model/map files if useful for reproducing this. Any guidance on what else to check (OpenMM installation, platform/GPU selection, log verbosity settings for more detail than "None") would be much appreciated John Guardado (he/him) | G1 PhD Student, BM CALIFORNIA INSTITUTE OF TECHNOLOGY

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How do i remove the ghost bonds?
by Francisco 04 Jul '26

04 Jul '26

open /path/to/foo.pdb hide atoms select (#1/A:15,35,52,101,129 :< 5) & protein show sel atoms cartoon suppressBackboneDisplay false and then zooming into the carboxy-term at L129 How do I hide the ghost bonds? (i.e. the bond between OXT and the end of the tube, which is not an atom, and the bond between the C atom and also the end of the tube..) Thanks

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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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