January 2026 - 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 1.11.1 crashing in ubuntu 24.04
by Antonio Vila Sanjurjo 02 Feb '26

02 Feb '26

Hello! I'm having problems installing ChimeraX version 1.11.1 in ubuntu 24.04. It crashes right after execution with the following terminal output __NV_PRIME_RENDER_OFFLOAD=1 __GLX_VENDOR_LIBRARY_NAME=nvidia chimerax --debug ... Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, psutil._psutil_linux, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, PIL._imaging, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler (total: 41) Aborted (core dumped) any ideas? best, Antón _______________________________________________________ Dr. Antón Vila-Sanjurjo Professor of Genetics phone: +34 881012267 email: anton.vila(a)udc.es Facultade de Ciencias e CICA - Centro Interdisciplinar de Química e Bioloxía UNIVERSIDADE DA CORUÑA As Carballeiras, s/n. Campus de Elviña. 15071 A Coruña, España [cid:9245848e-8b33-492c-b28b-ec67d05de404]

2 1

Question about DNA representation
by Enrico Martinez 29 Jan '26

29 Jan '26

Dear ChimeraX users! I have a question regarding the representation of DNA. In my input structure, the terminal base pairs are not involved in complementary pairing. When I display the entire DNA using atom activation stubs (with nucleotides ladder showStubs true), these terminal residues appear unconnected. I've tried hiding the stubs using the same command for selected terminal residues, but it also affects the entire DNA globally rather than just the terminal residues, e.g.: nucleotides sel ladder showStubs false How could I find the stubs for the selected residues only? Many thanks in advance! Enrico

2 4

Question about ligand protonation
by Enrico Martinez 28 Jan '26

28 Jan '26

Dear ChimeraX users! I have a question about the protonation of ligands in the complex. When I protonate only a ligand (using addh :LIG) I see in the log that it takes into account the hydrogen bonds. Does it mean that it defines the protonation state of each titratable group based on its local chemical environment of binding pocket? If so, is it possible to manually define the total charge of the ligand (and protonate it according to it)? Many thanks in advance! Enrico

2 3

Color by custom attribute
by Juan Ortiz Mateu 28 Jan '26

28 Jan '26

Dear ChimeraX team, I’ve created a .deffatr file to color residues in a chain by a custom attribute (attached). It seems that ChimeraX opens it correctly: open <help:user/commands/open.html> "/Users/ortizmateujuan/MEGA/MEGAsync/MemProtLab_UV/PROYECTOS LAB/Proyecto F1L VaccV/Alphafold/scanF1L.defattr" Summary of feedback from opening /Users/ortizmateujuan/MEGA/MEGAsync/MemProtLab_UV/PROYECTOS LAB/Proyecto F1L VaccV/Alphafold/scanF1L.defattr note Assigned attribute 'ld50' to 17 residues using match mode: 1-to-1 However, when I go to Render/Select by attribute, it does not appear on the list, and when I try with commands it says: color byattribute <help:user/commands/color.html#byattribute> ld50 palette ^rdylbu No known/registered numeric attribute ld50 Could you help me with this? Thank you very much. PS. I want to unsubscribe to this mailing list. I have tried emailing chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> many times but I keep receiving these emails. Could you do it for me please? Thanks again. ______________________ Juan Ortiz Mateu Researcher PhD Student Membrane Proteins Lab Biotecmed Institute University of Valencia Av. Vicent Andrés Estellés, 19 46100 Burjassot (Valencia) Spain research.uv.es/membrana/

2 1

Saving structures
by Timothy Springer 27 Jan '26

27 Jan '26

What am I doing wrong? save midas.pdb format pdb models #1/B:1101@MG saves the entire #1 structure rather than the single atom. I have a similar problem using combine. I issue a cd command in .cxc files. But at some point during sessions, the directory switches to my home directory. I have to frequently issue the cd command. - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

3 7

morph command
by Matzov Donna 27 Jan '26

27 Jan '26

Hello, I'm trying to morph two conformations of the same protein in which one of the helices moves while it rotates. I used the following command: #morph #1,2 frames 101 wrap t method linear minHingeSpacing 20 While moving from one state to the other, the helix mentioned above is distorted (it starts and end looking good but in the middle it loses it's helical shape). Could I add/change on of the parameters to fix that? Many thanks, Donna Matzov, PhD Department of Structural Biology Weizmann Institute of Science The Shalev-Benami Lab<https://www.weizmann.ac.il/Structural_Biology/Shalev-Benami/home>

2 1