January 2026 - ChimeraX-users - RBVI Mailing Lists

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

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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>

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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

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viewdockx
by Bäse, Nico 26 Jan '26

26 Jan '26

Dear ChimeraX developers, I would like to visualize my docking results from swissdock. But when I open viewdockx, I always get an error No suitable models found for ViewDockX. Can You help me? ___________________________________________ Kind Regards / Mit freundlichen Grüßen M.Sc. Nico Bäse Doktorand Institut für Pflanzenwissenschaften und Mikrobiologie Mikrobiologie und Biotechnologie Ohnhorststr. 18 22609 Hamburg Raum: 3.046, Otto-Warburg-Haus Tel.: <tel:+49-40-428-16-532> +49 40 428 16 521 E-Mail: <mailto:nico.baese@uni-hamburg.de> nico.baese(a)uni-hamburg.de

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Filtering solvent in MD trajectories
by Enrico Martinez 23 Jan '26

23 Jan '26

Dear ChimeraX users! I am working on the visualization of an MD trajectory where some water molecules are broken due to PBC artifacts, causing oxygen and hydrogen atoms to be separated over large distances. To address this, I currently use the following workflow: 1. Remove all bonds in water molecules near the ligand. 2. Rebuild only reasonable bonds, avoiding artifactually long bonds. 3. Remove water atoms that have no bonds per frame: perframe "~bond :HOH & :LIG :<5.0; bond :HOH & :LIG :<5.0 reasonable true; hide :HOH & @@num_bonds=0 target a" interval 1 This works well to fix visualization artifacts, but the workflow is computationally heavy, as it rebuilds bonds in every frame. Is there a way to achieve the same in a single step by simply removing waters with stretched bonds? Many thanks in advance! Enrico

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named selection
by Timothy Springer 23 Jan '26

23 Jan '26

I cant get my named selections to work. Here is an example. select #1/V:80@CD2 1 atom, 1 residue, 1 model selected name test sel select clear select test Nothing selected - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

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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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possible bug in map segmentation?
by Alexis Rohou 23 Jan '26

23 Jan '26

Hi all, I'm seeing unexpected behavior when I do the following: - open PDB A and corresponding MRC map A (models #1 and #2) - open PDB B and corresponding MRC map B (models #3 and #4) - match #3 to #1 bring #4 - use the "Segment Map" GUI tool to perform segmentation on #4 with default parameters except "Display at most" set to 160 and "Group by selectivity" selected instead of "Group by smoothing" The unexpected behavior is that the segmentation surfaces are all offset from the map. It looks to me like the segmentation was performed on the map as though it had never been shifted/rotated by the match command. This is with ChimeraX-1.10. My apologies - I've not had time to test whether the same happens with the latest version of ChimeraX, nor to come up with an open-source, sharable example. Cheers, Alexis

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ChimeraX for 3D Model of Mitochondrion
by Wilson, Melissa (NIH/NINDS) [F] 22 Jan '26

22 Jan '26

Hello, I have a stack of serial electron microscopy images in which I segmented one single mitolysosme (basically a mitochondrion being degraded) across all the images in napari. My goal now is to create a 3D reconstruction of the mitolysosome from all the stacks. Napari hasn't been working the way I'd like. I see a lot of protein structures used in your program. Can this program support visualization of larger structures -like this organelle? Sincerely, Melissa

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how MatchMaker computes RMSD and alignment scores
by EMMANUEL JAIME SIBAYAN 20 Jan '26

20 Jan '26

Dear ChimeraX Team, Dear ChimeraX Team, Thank you for the documentation on the MatchMaker tool. It explains well how the tool works. I would like to ask a very simple clarification for my thesis: How are the numerical values reported by MatchMaker actually calculated? Specifically: 1. What is the mathematical formula used to compute RMSD, and which atoms are used by default? 2. How does MatchMaker convert protein sequences into numerical alignment scores? 3. Is the alignment score simply a sum of substitution matrix values, secondary-structure scores, and gap penalties, or is it weighted or normalized? I just want to clearly explain how these numbers are obtained. Thank you very much. Best regards, Emmanuel Jaime S. Sibayan -- *The information or attachment(s) in this email is(are) strictly confidential and is(are) for the intended recipient only. Any unauthorized use, dissemination, or copy of this message or the information it contains is prohibited. The recipient has the responsibility to ensure the protection of any personal data included in this e-mail and its attachment(s). If you are not the intended recipient or you receive this email by mistake, please notify the sender immediately and delete the original message and attachment(s).*

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