June 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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boltz latest version with ChimeraX1.10
by svle＠tiscali.it 24 Jul '25

24 Jul '25

Hi, it is possible to install the latest version ( 2.1.1 ) of boltz in ChimeraX 1.10 with the command boltz install? Thanks. Saverio

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Model grouping and next/previous buttons
by Oliver Clarke 02 Jul '25

02 Jul '25

Hi, I use the next/previous buttons (sequential display controls) in the model panel quite a lot for quickly flicking between 3D classes - they are very handy for this! I would like to be able to use the same buttons for switching between model/map pairs, but there is no way to do this currently. I expected that if I grouped models by using the rename command to make (for example) the map a sub-model (e.g. model #1, map #1.1), then the next/prev buttons would switch between the model groupings, but this is not the case - it still treats the sub-models as independent models. Would it be possible to revisit this logic so that if a "base-level" model like #1 is selected, next/prev will switch between model groupings, while if a member of an ensemble is selected (say #1.1), it will cycle through members of the ensemble? Also, would it be possible at some point to add a GUI option for grouping models - perhaps a button in the model panel that allows for automatic grouping of the selected models? Cheers Oli

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Query for Volume viewer
by Akash Singh 01 Jul '25

01 Jul '25

Hi, I'm a researcher from India. I have been trying to make some EM fitting image with model protein. There is no Volume viewer option for Line smoothening, surface smoothening or square mesh to triangle mesh conversion. Also surface smoothening problem. I have been trying to execute through the command line, but it doesnt work . Can you help me regarding command line code for following Mesh Line smoothing Mesh surface smoothening Dim transparency The suite is ChimeraX or ChimeraX 1.9 Regards, Akash Singh

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Filling gaps in selection
by Bruno Hay Mele 30 Jun '25

30 Jun '25

Hi all, I'm trying to evaluate salient differences within a specific topological domain across a set of protein structures. My workflow is as follows: I choose a reference structure, and use MatchMaker to align all other structures to it. Then, I use the Contacts tool with distance 0 and overlap 0 to select CAs of residues that are perfectly aligned to the reference selection (i.e. the topological domain). This approach works well in conserved regions, but it results in gaps where insertions or small variations occur. I've tried to use sel up to fill these gaps, but my attempts have failed miserably. Is there a way to fill in gaps within a discontinuous selectionbi.e., to make it continuousbwithout extending the selection outward beyond the domain of interest? Ideally, I'd like to interpolate or bridge only the missing parts, without picking up unrelated residues. cheers, -- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118

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