August 2025 - ChimeraX-users - RBVI Mailing Lists

An error opening chimerax seesion
by Yehuda Halfon 11 Mar '26

11 Mar '26

Hi all, I'm using chimeraX 0.8 (2018-12-17) on centos 7 (can't remember the build). Sometimes when I load a session that was saved using this version of chimeraX it gives me this error: Unable to restore session, resetting. Traceback (most recent call last): File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/core/ session.py", line 593, in restore obj = sm.restore_snapshot(self, data) File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/ std_commands/view.py", line 214, in restore_snapshot for k,v in data ['view attrs'].items(): TypeError: 'NoneType' object is not subscriptable After that I can't open the session again, so I need to remake it. Help, Yehuda Halfon

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VR on ubuntu workstation
by arangarajan＠initialtx.com 04 Mar '26

04 Mar '26

Hi, i got steam VR installed but later found out that Oculus does not support linux. Is there a work around for using chimerax VR on latest ubuntu machine with oculus rift s headset? i can get other headset also if it will fit this purpose. thanks in advance, best amith

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ISOLDE and secondary structure restraints
by Guido Hansen 02 Mar '26

02 Mar '26

Hi all, I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess: Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script? Cheers, Guido -- PD Dr. Guido Hansen Group Leader UNIVERSITÄT ZU LÜBECK INSTITUT FÜR BIOCHEMIE Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen(a)biochem.uni-luebeck.de www.biochem.uni-luebeck.de [1] Ratzeburger Allee 160 23562 Lübeck Links: ------ [1] http://www.biochem.uni-luebeck.de

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Volume eraser as cube?
by Oliver Clarke 25 Feb '26

25 Feb '26

Hi all, Hope the chimeraX team & community are having a great start to 2025! There are often situations (in single particle cryo-EM) where I would like to erase using a plane rather than a sphere - e.g., when I want to chop off density protruding from a nanodisc or micelle in order to make a mask. There are various workaround ways to do this (e.g. just making the sphere enormous, making a cubic/rectangular mask and multiplying/substracting, etc), but I was wondering if this is a common enough scenario (perhaps other users can chime in?) that it might be worth adding the option of erasing using a cube rather than a sphere? Cheers Oli

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ChimeraX version 1.9 has been released
by Elaine Meng 23 Jan '26

23 Jan '26

UCSF ChimeraX version 1.9 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html Updates since version 1.8 (June 2024) include: - Foldseek search and analysis of large sets of similar structures - Find Cavities tool and "kvfinder" command to identify pockets and channels in macromolecules - optional residue-level summaries of H-bond and contact calculations - "mutationscores" command for analysis and plotting of results from deep mutational scanning - "surface hidefarblobs" command for colocalization analysis of light microscopy channels - raycasting option for medical images or other maps displayed as transparent volumes - selection can be expanded to all residues associated with the same column(s) in a sequence alignment - protein structure metadata can be updated with full chain sequences - missing-structure pseudobonds are labeled with the number of missing residues (default, can be turned off in preferences) For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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Focus in ChimeraX
by Luca Pellegrini 10 Oct '25

10 Oct '25

Hi, What is the ChimeraX equivalent to the Focus command in Chimera? I have selected a portion of a structure, and would like to bring it into focus without dragging it into view. Also Focus would automatically set the selection as the pivot point. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA lp212(a)cam.ac.uk

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Monitor distance throughout the trajectory
by Alexandra Zahradnikova 05 Sep '25

05 Sep '25

Hi I would like to record the evolution of distance between two atoms along all points of a MD trajectory into a file but I cannot find a command to keep saving/displaying the distance in the log for the whole trajectory, just for individual points (although of course the actual distance is shown in the GUI when the trajectory is played). Thanks in advance for help. Best regards Sasha

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Minimize structure capability in chimeraX?
by Kabir Gupta 02 Sep '25

02 Sep '25

Hi all, Does ChimeraX currently have the capability to minimize a structure? The functionality I'm talking about is of the sort available under Tools -> Structure Editing -> Minimize Structure... in the original Chimera. Last I can find is from a mail thread in 2020, at which point this had not yet been implemented in ChimeraX. Is there an acceptable substitute to achieve the same thing now, or do I have to reopen in original Chimera to do minimizations? Thanks very much, Kabir

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Publication Request
by Russell Couch 29 Aug '25

29 Aug '25

Hello UCSF! My name is Russell and I am a 17 year old student seeking approval from the developers to use ChimeraX in the publication of educationally-intended (not commercially-intended) content I would like to design using the program and animate separately. I would like to use ChimeraX to, for example, compile individual proteins into a complete infectious pathogen in order to demonstrate the roles of individual proteins in the process of infection, disease progression, and possible treatment. I want to firmly state that my personal purpose of the publication is educational, though I understand YouTube is inherently a commercial platform. When complete, the videos would be uploaded to a brand new, unmonetized channel dedicated to my educational publications. There would be no other co-collaborators, as in people frequently working with me and using ChimeraX to produce educational content. This is a personal project and I would be the only one using the program to produce my content. If another creator wanted to collaborate with me using their own research and resources (assuming they have all the proper permission like I'm asking for), would that be allowed, assuming the collaboration is occasional and on a per-video basis rather than consistent or unifying, such as two channels deciding to join together? On a bit of a more personal note, I am applying to college soon and am very interested in a couple of colleges in California. I am very passionate about engineering, particularly chemical engineering, and I believe the cures of tomorrow are waiting to be discovered. I am on a mission to discover them and make them available to all. While I am determined to be the change I want to be no matter where I go, I would like to attend a good engineering school if possible, and am personally very attracted to the idea of going to college in California. Some of the very best engineering schools in the country are in California, and getting into them would be a dream come true, though I am realistic and prepared to achieve my goals without any of their external resources. These resources, while valuable, mean nothing without the internal drive to strive. Regardless of acceptance, the colleges in California most intriguing to me are UCB, Caltech, and Stanford, though UCSD, Irvine, Davis, and many other schools there all have fantastic engineering programs, and are more statistically favorable in terms of acceptance, though still quite selective. I know UCSF is a medical school, but it shares with these colleges very high selectivity, and I would love to gather any potential advice, especially coming directly from another top college. I greatly appreciate you taking the time to read my request and am very excited to use ChimeraX, whether for personal or educational use. Sincerely, Russell Couch

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Coloring different regions
by Vojo P Deretic 29 Aug '25

29 Aug '25

Hi How to color different domains in a structure in ChineraX. I tried selecting residues on the sequence and can get an outline over the selection but how do I color different regions and keep all of them differently colored plus save the work? Thanks Sent from my iPhone with lots of typos and autocorrect nonsense - my apologies...

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