September 2026 - ChimeraX-users - RBVI Mailing Lists

(no subject)
by 张晓飞 19 Sep '26

19 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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How to redock the toolbar right below the menu
by Zakia Nishat 03 Sep '26

03 Sep '26

Hi, I somehow undocked the toolbar from the main window, now cannot redock it, even if I am dragging and trying to drop in the exact place, it's not working, it rather replaces the entire chimerax window. https://drive.google.com/file/d/1N329e0RGrX3tD1SBN7Xz6WdAsIrQ7d6P/view?usp=… Please see the video attached. Please tell me how can reset this. The toolbar is docking on the left side menu, but I really want it where it was before. Best, Zakia

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ARM on Windows
by tolung.bio＠gmail.com 01 Sep '26

01 Sep '26

Hello ChimeraX team, With the upcoming nVidia RTX Spark platform, I am starting to consider making the switch to the ARM CPUs. However, I am hesitant about the potential software incompatibilities. And of course, ChimeraX is one of the software that must run on my computer without any issues. Although Windows 11 is supposed to run x86 code via emulation, I see all sorts of issues mentiones, such as the certain versions of ChimeraX not running on Windows ARM through the emulator mentioned in this forum about a year ago. Since you already have an ARM distribution for Macs, are you also planning to release a native ARM version for windows, too? If so, what is the rough estimated timeline we may expect to see it? Thanks, Gökhan

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