September 2026 - ChimeraX-users - RBVI Mailing Lists

MCP for ChimeraX
by Alexis Rohou 20 Oct '26

20 Oct '26

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

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morph command ignores ions in metalloproteins?
by Guillaume Gaullier 02 Oct '26

02 Oct '26

Hello, I am trying to make a morph between PDB entries 9SKS and 9SKT. The protein does what I want, but I can't find out how to include the active site :ZN in the interpolation. This ion is consistently numbered between both structures, and I give model numbers to the morph command, which should select the entire models including their ions. Nothing about this in the documentation. What am I missing? If interpolating ions with morph is impossible to do for some reason, then it would be helpful to list it in the "limitations" section<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/morph.html#limitations> of the command's documentation. Thank you in advance, Guillaume --- Guillaume Gaullier, PhD Researcher, Blikstad group Molecular Biomimetics / Microbial Chemistry Department of Chemistry - Ångström Uppsala University Regementsvägen 10 752 37 Uppsala Sweden 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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Windows 11 DDL load failures
by Greg Couch 30 Sep '26

30 Sep '26

On Windows 11, if you are getting "DLL load failed while importing" errors, we think we have fixed it in the daily builds. So please switch to a daily build until 1.13 comes out. Supposedly, this error will go away on its own over time. But if you can't wait, or can't switch, for example, you're using the ISOLDE bundle, you'll need to either (a) turn off Smart App Control (not recommended), (b) turn on developer mode (not recommended), or (c) unblock the particular DLL. See the AI answer with PowerShell Unlock-File at https://learn.microsoft.com/en-nz/answers/questions/5765803/unblock-a-file-…. -- Greg

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Re: What Should You Consider When Comparing CDM Grow Lights?
by Eric Pettersen 27 Sep '26

27 Sep '26

Sorry about this message -- there was a moderation mishap. --Eric > On Sep 25, 2026, at 11:54 PM, lucasblake686--- via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > I’ve been looking into different lighting options for indoor growing and wanted to learn more about CDM systems. There are several factors worth considering, including wattage, coverage, heat output, reflector compatibility, and how the light fits with the rest of the growing setup. > > I found this collection while comparing available options: https://hydro-land.co.uk/collection/lighting/cdm-grow-lights/ > > For anyone who has experience with CDM lighting, what do you usually check before choosing a particular model? Is coverage or heat management the bigger consideration for your setup? > _______________________________________________ > 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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Problems with displaying atoms
by Barry Kesner 24 Sep '26

24 Sep '26

Hi, On windows 11 using chimera 1.12 I I had to modify an RNA structure by adding a 5’ G. Then I used Isolde to relax the region. However, after creating the new bond I was not able to see the atoms for the 2nd G. And after the simulation I was not able to display the atoms for almost all residues except for a select few! The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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How do I install bundles.
by Allen Place 22 Sep '26

22 Sep '26

I am trying to run my student’s imaging of our some proteins by running the .cxs file I was sent. I am getting the following error. To restore session: install Scenes bundle version 0.3.1 or newer install Animations bundle version 1.0 or newer How do I install these bundles? It is unclear how I do this/ Al

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(no subject)
by 张晓飞 18 Sep '26

18 Sep '26

您好：我与2026年9月14日使用ChimeraX 1.12软件的web service中提交了Job L7VGGZ7PMNMYBWAR（modeller refine 补 9IM3 十二聚体 12 条链的 internal missing loops，~4800 残基）：status = failed，stderr 为空，stdout 在键角违反列表中途截断、无 models summary，IL00010001.pdb和 B99990001.pdb 存在但 DL00010001.pdb 不存在，其中 B99990001.pdb12条链都在，并无缺失残基，但是残基编号直接从1-6564，并未按链划分。疑似计算时长超过服务器任务上限被强制终止。请问该服务是否有单任务时限？此类多链任务是否建议分链提交？B99990001.pdb 是否可以作为补全残基后的结构使用？十分期待能够收到您的回复，谢谢。张晓飞 202521100284(a)stu.ujn.edu.cn

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(no subject)
by 张晓飞 17 Sep '26

17 Sep '26

您好：我与2026年9月14日使用ChimeraX 1.12软件的web service中提交了Job L7VGGZ7PMNMYBWAR（modeller refine 补 9IM3 十二聚体 12 条链的 internal missing loops，~4800 残基）：status = failed，stderr 为空，stdout 在键角违反列表中途截断、无 models summary，IL00010001.pdb和 B99990001.pdb 存在但 DL00010001.pdb 不存在，其中 B99990001.pdb12条链都在，并无缺失残基，但是残基编号直接从1-6564，并未按链划分。疑似计算时长超过服务器任务上限被强制终止。请问该服务是否有单任务时限？此类多链任务是否建议分链提交？B99990001.pdb 是否可以作为补全残基后的结构使用？十分期待能够收到您的回复，谢谢。张晓飞 202521100284(a)stu.ujn.edu.cn

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addh - metalDist suppression & hbond treatment of aromatic amino groups
by Wes Dennis 15 Sep '26

15 Sep '26

Hello, We're using ChimeraX for structural analysis of the 23S rRNA peptidyl transferase centre in 1VY4 (2.60 Å, two 70S copies). We ran addh on the full deposition and found that thirteen base amino and imino nitrogens received no hydrogen. All thirteen sit 2.68–3.54 Å from a modelled magnesium, so metalDist is the obvious explanation, and we've since restored those protons from chemistry templates for downstream work. We're now trying to understand precisely what addh did rather than infer it, and four questions would help. Not reporting a bug — the behaviour looks correct, we just can't tell from the documentation which of several readings is right. *1.* Is there any way to obtain the list of hydrogens addh declined to add under metalDist, together with the X–H–M angle it computed for each? A log option, a return value, an attribute. Failing that, is the suppression recorded anywhere at all — even as a count? *2.* For which functional groups does hbond true actually adjust hydrogen position? Specifically, is an aromatic exocyclic amino — adenine N6, cytosine N4, guanine N2 — treated as rotatable about the C–N bond, or are its two hydrogens fixed by the heavy-atom geometry? If adjustable, is the adjustment confined to the base plane or can it go out of plane? The hbonds documentation describes well-determined groups versus rotatable hydroxyls, and we're unsure which side an aromatic amino falls on — and whether that page's criteria apply to addh's hbond option at all. *3.* The documentation says a hydrogen is suppressed if the X–H–M angle *would be* >120°. At what position is that angle evaluated — the position addh would have chosen with hbond optimisation applied, or a geometry-only position before optimisation? *4.* For an exocyclic amino group, how are H61/H62, H41/H42 and H21/H22 assigned to the two hydrogen positions — deterministically from the 3D coordinates, or by a fixed convention relative to the ring? Related: is metalDist evaluated per candidate hydrogen? We see nitrogens where one hydrogen was added and the other was not, which the documentation doesn't address, and if so we'd like to know whether the surviving hydrogen keeps a stable name. We have several further questions in the same area but didn't want to send a wall of them. Happy to follow up separately if that's welcome. Thanks for ChimeraX, and for the documentation generally — it's better than most. Wes Dennis Independent researcher

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compact toolbar button
by Alpay S 11 Sep '26

11 Sep '26

Dear ChimeraX developers, Is it possible to add compact buttons to custom toolbars like this in main ChimeraX? I can only create full size buttons like the ones in the "Lighting & Effects" section. I saw compact as a provider attribute only on the development branch but not in the main branch. Regards [image: image.png] [image: image.png]

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