- ChimeraX-users - RBVI Mailing Lists

Is toolshed down?
by jurkeviciute.gabija＠gmail.com 06 Jan '26

06 Jan '26

Hi, Apologies to bother, but I cannot seem to access toolshed to install isolde on either chimerax 1.11 or my web browser. I checked in with some colleagues and they reported the same thing. Is the site down for the toolshed by any chance? Thanks! Gabija

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Video Tutorial on Protein Interaction Modeling
by David S. Fay 05 Jan '26

05 Jan '26

Hi Everyone, Despite not really being qualified, I’ve done several protein modeling workshops at universities over the past year with some positive responses. It seems to be quite useful to a good number of scientists like myself (clueless molecular/cellular biologists etc), and in particular for less experienced users. Part of my ability to pull this off at any level has been the help I’ve received from others including the wonderful staff the ChimeraX, who I give ample props to in the video. Anyway, feel free to share with students or others who might find this useful. It’s rather long (97 minutes) and I do go into a fair bit of detail about how ipTM is determined along with some of the recently developed alternative metrics for scoring protein-protein interactions. I’ve attached the link below. I also realize that this user group is very sophisticated, so feel free to comment or correct and to add to anything I may have missed or not stated properly. Thanks and happy new year, David David S. Fay Ph.D. Professor, Department of Molecular Biology Director (PD/PI), National Institutes of Health Wyoming INBRE University of Wyoming email: davidfay(a)uwyo.edu<mailto:davidfay@uwyo.edu> <https://youtu.be/u63oYfWDBoM> [maxresdefault.jpg] David's AlphaFold WorkShop 2026<https://youtu.be/u63oYfWDBoM> youtu.be<https://youtu.be/u63oYfWDBoM>

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Boltz affinity prediction
by George Tzotzos 03 Jan '26

03 Jan '26

Happy New Year to all I’m unable to find out how to obtain Boltz binding affinity predictions. Probably, I’m missing out something. Any help would be most welcome. I’m attaching a screenshot for easy diagnostics. Many thanks

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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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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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