January 2026 - ChimeraX-users - RBVI Mailing Lists

Surface overlapping with atomic model
by naeshi9min＠postech.ac.kr 07 Jan '26

07 Jan '26

Hi, I'm Gumin Han from South Korea. Thank you for your wonderful visualization tools. This is my first time writing a question here. I want to overlap my models with surface as shown in the link (Figure panel B) https://www.nature.com/articles/s41467-024-49516-2/figures/1 Which options should I use? Thank you for reading my E-mail and best wishes for the New Year' Best regards, 2026, Jan 7th Gumin Han

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Trouble installing ISOLDE in ChimeraX
by Heng Jiang 06 Jan '26

06 Jan '26

Dear ChimeraX Support Team, I hope this message finds you well. I am currently trying to install the ISOLDE plugin in UCSF ChimeraX via Tools → More Tools…, but unfortunately, the installation does not work. I have attempted multiple approaches, but the “More Tools” window does not open. Could you please advise if there is an alternative way to install ISOLDE, such as an offline installation method or by providing the necessary plugin files directly? Thank you very much for your time and assistance. I look forward to your reply. Best regards, Heng Jiang

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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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