January 2026 - ChimeraX-users - RBVI Mailing Lists

Question about ligand protonation
by Enrico Martinez 24 Jan '26

24 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

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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 22 Jan '26

22 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 19 Jan '26

19 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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Problem in Chimerax 1.11
by Angelika Dibijo 19 Jan '26

19 Jan '26

Hi Chimerax Team, Could you please assist me in making ChimeraX 1.11 work on my machine? It was built without error from GitLab. ./ChimeraX --version UCSF ChimeraX version: 1.12.dev202601140146 (2026-01-14) © 2016-2026 Regents of the University of California. All rights reserved. My machine is: nvidia-smi +-----------------------------------------------------------------------------------------+ | NVIDIA-SMI 570.195.03 Driver Version: 570.195.03 CUDA Version: 12.8 | |-----------------------------------------+------------------------+----------------------+ | GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |=========================================+========================+======================| | 0 NVIDIA L4 On | 00000000:E5:00.0 Off | 0 | | N/A 36C P8 15W / 72W | 45MiB / 23034MiB | 0% Default | | | | N/A | +-----------------------------------------+------------------------+----------------------+ +-----------------------------------------------------------------------------------------+ | Processes: | | GPU GI CI PID Type Process name GPU Memory | | ID ID Usage | |=========================================================================================| | 0 N/A N/A 1877027 G /usr/libexec/Xorg 39MiB | +-----------------------------------------------------------------------------------------+ The window pops up, then crashes as below. $ module load virtualgl Loading virtualgl/2.5.0 Loading requirement: libjpeg-turbo/1.4.2 $ vglrun ./ChimeraX NOTE: available bundle cache has not been initialized yet WARNING: GBM is not supported with the current configuration. Fallback to Vulkan rendering in Chromium. [1896428:1897552:0115/140239.807851:ERROR:gl_surface_egl.cc(303)] No suitable EGL configs found. [1896428:1897552:0115/140239.807872:ERROR:gl_context_egl.cc(159)] Failed to get config for surface 0 [1896428:1897552:0115/140239.807885:ERROR:gl_surface_egl.cc(303)] No suitable EGL configs found. [1896428:1897552:0115/140239.807889:ERROR:gl_surface_egl.cc(1018)] No suitable EGL configs found for initialization. [1896428:1897552:0115/140239.807892:ERROR:gpu_info_collector.cc(85)] gl::GLContext::CreateOffscreenGLSurface failed [1896428:1897552:0115/140239.807895:ERROR:gpu_info_collector.cc(597)] Could not create surface for info collection. [1896428:1897552:0115/140239.808002:ERROR:gl_surface_egl.cc(303)] No suitable EGL configs found. [1896428:1897552:0115/140239.808006:ERROR:gl_surface_egl.cc(1018)] No suitable EGL configs found for initialization. [1896428:1897552:0115/140239.808062:ERROR:gl_surface_egl.cc(303)] No suitable EGL configs found. [1896428:1897552:0115/140239.808065:ERROR:gl_surface_egl.cc(1018)] No suitable EGL configs found for initialization. [1896428:1897552:0115/140239.808068:ERROR:gpu_info_collector.cc(85)] gl::GLContext::CreateOffscreenGLSurface failed [1896428:1897552:0115/140239.808070:ERROR:gpu_info_collector.cc(597)] Could not create surface for info collection. Fatal Python error: Segmentation fault Thread 0x00007f62af7fe640 (most recent call first): File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/ssl.py", line 1382 in do_handshake File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/ssl.py", line 1104 in _create File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/ssl.py", line 517 in wrap_socket File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/http/client.py", line 1475 in connect File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/http/client.py", line 996 in send File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/http/client.py", line 1058 in _send_output File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/http/client.py", line 1298 in endheaders File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/http/client.py", line 1349 in _send_request File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/http/client.py", line 1303 in request File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/urllib/request.py", line 1348 in do_open File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/urllib/request.py", line 1391 in https_open File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/urllib/request.py", line 496 in _call_chain File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/urllib/request.py", line 536 in _open File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/urllib/request.py", line 519 in open File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/urllib/request.py", line 216 in urlopen File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/site-packages/chimerax/core/toolshed/available.py", line 62 in load File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 516 in reload_available File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/threading.py", line 982 in run File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/threading.py", line 1002 in _bootstrap Thread 0x00007f6378614740 (most recent call first): File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init File "/apps/src/CHIMERAX/src/ChimeraX/ChimeraX.app/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 in <module> File "<frozen runpy>", line 88 in _run_code File "<frozen runpy>", line 198 in _run_module_as_main 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, chimerax.pdb_lib._load_libs, PIL._imaging, 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) Segmentation fault (core dumped) Thank you so much. Please let me know if you need more information. Regards, Angel -- *ANGELIKA DIBIJO* System Administrator *Monash eResearch* Monash University, Clayton Campus M: + 61 426371313 E: angelika.dibijo(a)monash.edu W: Monash-eResearch <http://www.monash.edu.au/eresearch> We acknowledge and pay respect to the Elders and Traditional Owners of the land on which our four Australian campuses stand.

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Boltz and multi align structures/ligands
by George Tzotzos 18 Jan '26

18 Jan '26

I’ve used the ChimeraX Boltz interface and obtained multiple models of the same ligand bound on to the same receptor. I’d like to find residues within 5A of the ligand. Of course, I can do this one at a time. I wonder if there’s a way to automate the process. Your help is much appreciated George

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extending selections
by Timothy Springer 16 Jan '26

16 Jan '26

Hi, I am trying to select multiple interactions and include them in a single named selection. Is there a better way than this? select zone #2/A 3.6 #2 residues true; name inter2A sel select zone #2/B 3.6 #2 residues true; name inter2B sel name inter2all inter2A | inter2B This does not seem to work for me and when I try to show the selection select inter2all *it says* Nothing selected I got something similar to work for hbonds hbonds #2/A restrict #2/B-G color black name hbond_inter2 hbonds #2/B restrict #2/C-G color black name hbond_inter2 hbonds #2/C restrict #2/D-G color black name hbond_inter2 hbonds #2/D restrict #2/E-G color black name hbond_inter2 hbonds #2/E restrict #2/F-G color black name hbond_inter2 hbonds #2/F restrict #2/G color black name hbond_inter2 - 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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