January 2026 - ChimeraX-users - RBVI Mailing Lists

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

Depicting residues as spheres and adjusting sphere dimeter
by George Tzotzos 27 Jan '26

27 Jan '26

Help will be much appreciated. I’m trying to depict residues as spheres of reduced dimeter. My commands are: select <help:user/commands/select.html> :9,11,33,38,49,50,51,52,53,64,65,66,101,105 117 atoms, 114 bonds, 14 residues, 1 model selected show <help:user/commands/show.html> sel style <help:user/commands/style.html> sel ball Changed 117 atom styles style <help:user/commands/style.html> sel sphere Changed 117 atom styles size <help:user/commands/size.html> sel ballScale 0.2 Changed 1 ball scales Likewise with: setattr <help:user/commands/setattr.html> m ballScale 0.3 create true Assigning ballScale attribute to 1 item Obviously the above commands are wrong as they fail to generate the desired effect Have a good day George

2 2

Map qScore - Chimera vs. ChimeraX
by Elaine Meng 26 Jan '26

26 Jan '26

Forwarding in case someone can help with the MapQ-speciic parts of this question. Thanks Elaine > Begin forwarded message: > > Subject: [Chimera] Chimera qScore > Date: January 25, 2026 at 10:23:00 PM PST > Cc: oliver.schanz(a)boehringer-ingelheim.com > > Dear Chimera team, > We are currently aligning our in‑house cryo‑EM structure validation with community standards and encountered an issue with reproducing Q‑scores: > The wwPDB references the original Chimera/MapQ implementation, but as Chimera is being phased out in favor of ChimeraX, we can no longer reproduce the original Q‑scores in ChimeraX. > We have already evaluated available alternatives: > ChimeraX Q‑score plugin: We observe systematic differences between Q‑scores from ChimeraX and values in wwPDB/EMDB reports. The plugin author (Tristan Croll) indicated that differences likely stem from sampling not matching the original implementation and possibly slightly different averaging. The tool has also not been actively maintained for some time. > Python implementations (e.g., jamaliki/qscore and an internal prototype): These likewise yield different Q‑scores on the same model–map pairs, likely for similar reasons. > Given this, we would appreciate your guidance on two points: > Are there plans to migrate the original Chimera/MapQ Q‑score implementation into ChimeraX? > If not (or not soon), would it be possible to obtain free or reduced‑cost access to Chimera solely for the purpose of Q‑score calculations? We are otherwise fully using ChimeraX in our workflow. > Thank you very much for your feedback. > Best regards, > Oliver Schanz > > > Oliver Schanz > IT Research, Development & Medicine > > Boehringer Ingelheim GmbH > Birkendorfer Str. 65 | 88397 Biberach > > T +49 (7351) 54-7299 <tel:+49 (7351) 54-7299> > M +49 (151) 15026220 <tel:+49 (151) 15026220> > E oliver.schanz(a)boehringer-ingelheim.com <mailto:oliver.schanz@boehringer-ingelheim.com>

2 1

changing default model display type
by Pranav Shah 26 Jan '26

26 Jan '26

Hi Team, I prefer to view my models represented in the classic ribbon-style. Is there a way I can make this a default behaviour in chimerax when opening an mmcif/pdb file? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

2 2