July 2026 - ChimeraX-users - RBVI Mailing Lists

Accelerate opening of AlphaFold models with ligands lacking a mmcif template?
by Ute Roehrig 25 Jul '26

25 Jul '26

Dear All, I am often opening AlphaFold 3 co-folding structures including small molecules in ChimeraX. In these models, ligands were provided as SMILES and are called LIG_X (with X being the chain label) in the AF3 output model.cif file. Opening these structures is very slow on my machine, because ChimeraX searches for a template for the ligands and finally fails with the warning "Unable to fetch template for 'LIG_X': will connect using distance criteria". Is there any workaround? E.g. by telling ChimeraX not to look for a template? Thank you for your help, Ute

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Re: downloading trouble
by Tom Goddard 22 Jul '26

22 Jul '26

Glad you got it to work. I think if a ChimeraX plugin says it requires ChimeraX version 12.0 then it will not be allowed to install on an older ChimeraX version like the 12.0 release candidates. Tom > On Jul 22, 2026, at 2:58 AM, jean-francois.gaucher(a)u-pariscite.fr wrote: > > Hi Tom, > > I just reinstalled the latest version of ChimeraX and it's working now. What a mystery! > > Thanks for your help. > > Have a good day, > > Jef > > > > Le 22/07/2026 à 03:02, Tom Goddard a écrit : >> Hi Jean-François, >> >> I don't know why the Install button for ISOLDE using ChimeraX menu Tools / More Tools... does nothing for you. I suggest updating to the current ChimeraX 1.12 release. You are using a 1.12 release candidate and the ISOLDE 1.12.0 version is for the ChimeraX 1.12 release. If that does not help you could download the ISOLDE distribution outside ChimeraX using a web browser from https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde and then in ChimeraX use the toolshed install command to install the downloaded .whl file. >> >> toolshed install ~/Downloads/chimerax_isolde-1.12.0-cp311-cp311-macosx_11_0_universal2.whl >> >> Tom >> >>> On Jul 21, 2026, at 3:15 AM, jean-francois.gaucher--- via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> <mailto:chimerax-users@cgl.ucsf.edu> wrote: >>> >>> Dear Sir, >>> >>> I am having trouble downloading version 1.12.0 of ISOLDE from the ChimeraX "toolshed" (using version 1.12rc202606020412 (2026-06-02), installed on an Intel-based MacBook Pro running Sequoia 15.7.7). >>> >>> When I click the "install" button, nothing happens. >>> >>> Is this a bug, or have I missed something? >>> >>> Thank you for developing the ISOLDE software and for your assistance. >>> >>> Best regards, >>> >>> Jean-François Gaucher >>> >>> -- >>> Jean-Francois GAUCHER >>> Universite de Paris Cite - UFR de pharmacie >>> Laboratoire Cibles Therapeutiques et Conception de Medicaments >>> (CiTCoM) UMR 8038 CNRS/UPD >>> 4, av. de l'Observatoire 75270 Paris CEDEX 06 >>> Tel +33(0)1 70 64 94 07 FAX +33(0)1 53 73 99 25 >>> e.mail : jean-francois.gaucher(a)u-pariscite.fr <mailto:jean-francois.gaucher@u-pariscite.fr> >>> https://www.researchgate.net/profile/Jean-Francois_Gaucher/ >>> https://www.citcom.cnrs.fr <https://www.citcom.cnrs.fr/> >>> orcid 0000-0002-8448-1491 >>> >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>> >> > -- > Jean-Francois GAUCHER > Universite de Paris Cite - UFR de pharmacie > Laboratoire Cibles Therapeutiques et Conception de Medicaments > (CiTCoM) UMR 8038 CNRS/UPD > 4, av. de l'Observatoire 75270 Paris CEDEX 06 > Tel +33(0)1 70 64 94 07 FAX +33(0)1 53 73 99 25 > e.mail : jean-francois.gaucher(a)u-pariscite.fr <mailto:jean-francois.gaucher@u-pariscite.fr> > https://www.researchgate.net/profile/Jean-Francois_Gaucher/ > https://www.citcom.cnrs.fr <https://www.citcom.cnrs.fr/> > orcid 0000-0002-8448-1491

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downloading trouble
by jean-francois.gaucher＠u-pariscite.fr 22 Jul '26

22 Jul '26

Dear Sir, I am having trouble downloading version 1.12.0 of ISOLDE from the ChimeraX "toolshed" (using version 1.12rc202606020412 (2026-06-02), installed on an Intel-based MacBook Pro running Sequoia 15.7.7). When I click the "install" button, nothing happens. Is this a bug, or have I missed something? Thank you for developing the ISOLDE software and for your assistance. Best regards, Jean-François Gaucher -- Jean-Francois GAUCHER Universite de Paris Cite - UFR de pharmacie Laboratoire Cibles Therapeutiques et Conception de Medicaments (CiTCoM) UMR 8038 CNRS/UPD 4, av. de l'Observatoire 75270 Paris CEDEX 06 Tel +33(0)1 70 64 94 07 FAX +33(0)1 53 73 99 25 e.mail : jean-francois.gaucher(a)u-pariscite.fr https://www.researchgate.net/profile/Jean-Francois_Gaucher/ https://www.citcom.cnrs.fr orcid 0000-0002-8448-1491

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ChimeraX packages cannot be installed on Debian testing due to libosmesa6/libnsl2 dependencies
by Bruno Hay Mele 21 Jul '26

21 Jul '26

Hi! I am unable to install any currently available ChimeraX release or daily build on my Debian testing because the Ubuntu packages depend on libraries that are no longer available in Debian testing. ucsf-chimerax_1.11.1ubuntu22.04_amd64.deb ucsf-chimerax_1.12ubuntu22.04_amd64.deb ucsf-chimerax-daily:amd64=2026.07.20ubuntu22.04 fail because I do not have/cannot install libnsl2, libosmesa6 ucsf-chimerax-daily:amd64=2026.07.20ubuntu24.04 fail because I do not have/cannot install libosmesa6 ucsf-chimerax-daily:amd64=2026.07.20ubuntu26.04 fail because I do not have/cannot install libc6 and libosmesa6 System information: Distribution: Debian GNU/Linux testing/forky Architecture: amd64 Kernel: 7.0.7+deb14-amd64 glibc: 2.42-17 GPU: Intel HD Graphics 4000, using the i915 driver Installed NIS library: libnsl3 2.0.1-2 Installed development package: libnsl-dev 2.0.1-2 Available SONAMEs: libnsl.so.3 libnsl.so.1 libnsl.so Not available from the configured Debian testing repositories: libnsl2 libosmesa6 libosmesa6-dev I am somewhat puzzled because, as far as I remember, both the production and daily builds were working on this same system until roughly two weeks ago. It is possible that a recent Debian testing upgrade removed or replaced the required compatibility libraries, so I may simply have been too aggressive in keeping the system fully up to date. -- Bruno Hay Mele, PhD https://github.com/bhym/

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using swapaa with custom built peptides
by Daniel Gurnon 20 Jul '26

20 Jul '26

Hi all, I occasionally use ChimeraX's "build structure" to construct short peptides to use in teaching. For efficiency's sake, it would be nice if I could take things I've already built and "mutate" an amino acid using the swapaa command. However, when I try to do this using a custom built structure (for example, selecting the residue I want to change, and then executing *swapaa sel arg*), I get the error "*No amino acid residues specified for swapping". * The command works for downloaded structures, just not the custom ones. Is there a missing attribute that swapaa checks for, that isn't created when you make a custom peptide? Dan ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135

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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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Change default molecule display to cartoon only (hide atoms)
by ramy.kazan＠ibpc.fr 09 Jul '26

09 Jul '26

Hi all, When I open a large model (e.g., a ribosome) in ChimeraX, the default display style shows it as atoms in the spheres style. I’d like to change this so that, by default, all atoms are hidden, and the model is displayed as a cartoon only. I’ve created an alias with the necessary commands and mapped it to a function key for quick adjustments. However, this approach has a limitation: after customizing one model (e.g., showing specific residues as atoms), opening a new model and using the function key overwrites the customized residues, applying the "cartoon-only" style to all open models. There must be a setting to adjust this behavior, but I haven’t been able to find it. I also recall reading that ChimeraX treats small and large models differently—perhaps based on the number of chains or residues—but I can’t remember the exact rules. Could someone point me to the correct way to set this as the default behavior for all new molecules? Thanks for your help! Best regards, Ramy

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A question for GPI-anchored protein
by 落合廣 09 Jul '26

09 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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