December 2025 - ChimeraX-users - RBVI Mailing Lists

help for RMSD
by marian.vincenzi 23 Dec '25

23 Dec '25

Dear Chimera staff, I am a PostDock from CNR-IBB of Naples (Italy). I am contacting you on the command "match" because I would use it to evaluate rmsd between two structures. I realized (maybe I am wrong) that the value given as output rises from the overlap only on C-alpha, but I used the command "match #1@n,ca,c,o to #2:904-976@n,ca,c,o". My aim was the RMSD evaluated on all backbone atoms and not only c-alpha. Is there anyway to get RMSD value on all backbone atome and overlap the two analysed structures ? Thank you in advance. While waiting, I wish all you team Merry Christmas and Happy New year :-) Marian

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New File Format for Recent ChimeraX Versions
by kkssy141＠gmail.com 22 Dec '25

22 Dec '25

Hello, I recall installing support for the XYZ file format by following the tutorial for older versions of ChimeraX, which worked as expected: https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_read_format… However, in recent ChimeraX versions (1.10 and 1.11), the same procedure no longer works. When running devel install, I encounter the below error message. I was wondering whether the documentation might need to be updated. Thanks. Best, Siyoung ``` devel install /Users/siyoungkim/Downloads/tut_read /Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: Freeware See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#licen… for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py running bdist_wheel installing to build/bdist.macosx-10.9-universal2/wheel running install running install_lib copying build/lib/chimerax/tut_read/io.py -> build/bdist.macosx-10.9-universal2/wheel/./chimerax/tut_read Traceback (most recent call last): File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/devel.py", line 180, in _run unbound_method(bb, *args, **kw) File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/bundle_builder/bundle_builder.py", line 165, in make_install _ = self.make_wheel(debug=debug) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/bundle_builder/bundle_builder.py", line 120, in make_wheel raise RuntimeError(f"Building wheel failed: {wheel}") RuntimeError: Building wheel failed: ChimeraX_TutorialReadFormat-0.1-py3-none-any.whl ```

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Re: ChimeraX Boltz prediction running eternally or failing submission to MSA server
by Arthur Kaser 22 Dec '25

22 Dec '25

Same here. Boltz2 appears to stall at api.colabfold.com<http://api.colabfold.com>, regardless of size/ length of the input sequence. Nil return at this step.

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Assistance with ChimeraX
by Vinita Pant 22 Dec '25

22 Dec '25

Dear ChimeraX Team, I am currently using ChimeraX 1.10.1 (2025-07-24) for preparing my protein for molecular docking, and I would like your guidance on repairing missing side chain atoms. I have explored several resources but have not yet found a solution. I appreciate any assistance you can provide to help me navigate this process effectively. Thank you for your support. *Thanks and Regards* *Vinita Pant* *Doctoral Student (SRF)* *ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal* *Mobile No.: +91 9536940943*

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how MatchMaker computes RMSD and alignment scores
by EMMANUEL JAIME SIBAYAN 22 Dec '25

22 Dec '25

Dear ChimeraX Team, Dear ChimeraX Team, Thank you for the documentation on the MatchMaker tool. It explains well how the tool works. I would like to ask a very simple clarification for my thesis: How are the numerical values reported by MatchMaker actually calculated? Specifically: 1. What is the mathematical formula used to compute RMSD, and which atoms are used by default? 2. How does MatchMaker convert protein sequences into numerical alignment scores? 3. Is the alignment score simply a sum of substitution matrix values, secondary-structure scores, and gap penalties, or is it weighted or normalized? I just want to clearly explain how these numbers are obtained. Thank you very much. Best regards, Emmanuel Jaime S. Sibayan -- *The information or attachment(s) in this email is(are) strictly confidential and is(are) for the intended recipient only. Any unauthorized use, dissemination, or copy of this message or the information it contains is prohibited. The recipient has the responsibility to ensure the protection of any personal data included in this e-mail and its attachment(s). If you are not the intended recipient or you receive this email by mistake, please notify the sender immediately and delete the original message and attachment(s).*

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Installing ChimeraX bundle with none Python file
by huybk81＠gmail.com 21 Dec '25

21 Dec '25

Hi, I am making a ChimeraX bundle. I need to read a csv file as template for the bundle. However, the template file (inside src folder) was not copied or added when installed. Is there anything that I should do to get it copied?

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Read CASTP pocket file
by George Tzotzos 19 Dec '25

19 Dec '25

Hi everybody, I’m following instructions in https://rbvi.github.io/chimerax-recipes/castp/castp.html open 1pn9 readcastp /Users/george/Downloads/1pn9/1pn9.poc and get Unknown command: readcastp /Users/george/Downloads/1pn9/1pn9.poc Any ideas why this is so. Many thanks George

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kvFinder tool
by George Tzotzos 19 Dec '25

19 Dec '25

I’ve opened 1PN9.pdb deleted all but chain A. I used kvfinder #1 probeIn 1.4 probeOut 4.0 The largest cavity has an ID 1.1.5. How does one identify the residues that line the cavity? Thank you

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Request for ChimeraX Installation Assistance
by CykaZH 19 Dec '25

19 Dec '25

Dear ChimeraX Team, I hope this message finds you well. I am writing to seek your assistance regarding the download of the latest version of ChimeraX. Currently, I am located in China, and the download speed for the software is extremely slow, even when using a VPN or an educational network. Additionally, when attempting to download via these methods, I encountered a page requiring a license, which prevented me from completing the download. To ensure a smoother and more efficient setup process, I would like to kindly ask if it would be possible for you to send the latest version of ChimeraX in .exe format as an email attachment. This would greatly help me avoid the download speed issues and the license-related obstacles I am currently facing. Thank you for your time and support. I truly appreciate your assistance and look forward to your response. Best regards, CykaZH Affiliated Hospital of Jiaxing University

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ChimeraX REST remotecontrol: CORS for localhost clients?
by Boris Steipe 18 Dec '25

18 Dec '25

Dear ChimeraX team - I am writing a local, interactive tutorial (Quarto HTML) that I want drive ChimeraX via the REST remotecontrol interface. I can send commands in JavaScript, but not read responses. Quarto serves my page locally - page origin: http://localhost:5779 - ChimeraX endpoint: http://127.0.0.1:61803/run?command=... ... but if I issue in the JS console: fetch("http://127.0.0.1:61803/run?command=help") .then(r => r.text()).then(console.log).catch(console.error); I get: Console error: - CORS blocked: “No ‘Access-Control-Allow-Origin’ header is present…” - Network panel shows 200 OK, but the Fetch promise rejects with TypeError: Failed to fetch. So: Is there a supported way (or could there be) for remotecontrol rest to emit CORS headers for localhost-only clients? Something like: - Access-Control-Allow-Origin: http://localhost:5779 (or a configurable allow-list, possibly including http://127.0.0.1:*) - Access-Control-Allow-Methods: GET, POST, OPTIONS - Access-Control-Allow-Headers: Content-Type - Handling preflight OPTIONS requests (e.g. relevant for POST ) - Even an "allow only loopback origins" mode would be sufficient. Ideally, enabling CORS would be controllable at runtime from within ChimeraX (e.g., as an option to remotecontrol rest start or a subsequent ChimeraX command), so that a teaching workflow can be fully self-contained. For example, something like: • remotecontrol rest start port 61803 cors allow-origin http://localhost:* • or: remotecontrol rest cors allow-origin http://localhost:* If there’s already an option/flag for this I would be grateful for pointers. (Or perhaps I have missed a recommended pattern.) Thank you! Boris (Nb. I do understand the security implications of CORS; this use case is strictly local (loopback only), with the goal to enable processing measurements/queries in browser-based teaching material. ) -- Boris Steipe MD, PhD Professor em. Department of Biochemistry Temerty Faculty of Medicine University of Toronto

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