November 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

4 6

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

3 6

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

6 9

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

3 2

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

3 4

bug report - pip list failure
by replacement2＠gmail.com 15 Dec '25

15 Dec '25

Hi, My apologies if this is not the best place to report a bug. There appears to be an issue with `pip list`, which may be caused by a typo in `pip.py`. Please see the traceback. It'd be great if someone can verify. Thanks. Traceback (most recent call last): File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute cmd.run(cmd_text) File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/pip.py", line 71, in pip pip_cmd.appendf("list") ^^^^^^^^^^^^^^^ AttributeError: 'list' object has no attribute 'appendf' cui5

4 4

Permission to create winget manifest?
by Joshua Raphael Uy 26 Nov '25

26 Nov '25

Hi Chimerax Dev team, My name is Josh Uy. I'm a graduate student at Arizona State University, and I frequently use ChimeraX as a visualization tool on both Windows and Linux! I'm wondering if you guys would be ok if I were to submit a winget <https://github.com/microsoft/winget-cli> manifest for ChimeraX? ChimeraX is a wonderful piece of software that I am using for my Ph.D and having an automated way to get and install via cli package manager tools would be incredibly handy to have. I wouldn't mind being the guy responsible for maintaining this if approved. Thank you, Josh Uy

2 1

Unable to restore session: need to install missing bundle
by GOVAERTS Cédric 25 Nov '25

25 Nov '25

Hi Team, I’m switching between computers and platforms, but now I try to reopen CXS session it fails and I get To restore session: install Animations bundle version 1.0 or newer Unable to restore session: need to install missing bundle I’ve tried the very last version of chimeraX (daily built). How can I solve this ? Thanks a bunch Cedric Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77<tel:+3226505377> Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

2 5

command history pulldown very short
by Alan Cheung 25 Nov '25

25 Nov '25

Hi There - i’m using chimerax on mac. Whenever i try to view my command history, either by tapping the up cursor or using the pop-out window, i can only ever recall 16 previous commands despite being set to remember 500 commands. However, the command file in ~/Library/Application Support/ChimeraX/commands contains (at least) 500 commands. Can you help? Alan

2 4

Unable to install boltz - please help
by Aggarwal, Aneel 25 Nov '25

25 Nov '25

Hello, I am a new user and trying to use boltz on my iMac (Tahoe OS) and get the error below. Any suggestions? Thanks, Aneel Successfully created Boltz Python virtual environment /Users/aneel/boltz22. Now installing Boltz and required packages from PyPi. This may take tens of of minutes since Boltz uses many other packages totaling about 1 Gbyte of disk space including torch, scipy, rdkit, llvmlite, sympy, pandas, numpy, wandb, numba... /Users/aneel/boltz22/bin/python -m pip install https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip Collecting https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip Using cached https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' INFO: pip is looking at multiple versions of boltz to determine which version is compatible with other requirements. This could take a while. ERROR: Could not find a version that satisfies the requirement torch==2.7.1 (from boltz) (from versions: 2.0.0, 2.0.1, 2.1.0, 2.1.1, 2.1.2, 2.2.0, 2.2.1, 2.2.2) ERROR: No matching distribution found for torch==2.7.1 [notice] A new release of pip is available: 24.0 -> 25.3 [notice] To update, run: /Users/aneel/boltz22/bin/python -m pip install --upgrade pip Boltz installation failed. See ChimeraX Log for details

3 5