- ChimeraX-users - RBVI Mailing Lists

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>

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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 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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Adjusting sphere radius
by George Tzotzos 16 Jan '26

16 Jan '26

I’ve issued the following commands for my models select <help:user/commands/select.html> #2/A:120,119,41,36,37,34,49,117 72 atoms, 68 bonds, 8 residues, 1 model selected setattr <help:user/commands/setattr.html> m ballScale 0.2 create true Assigning ballScale attribute to 2 items No changes were observed on the ball scale. Is it likely that I should be trying something different to change the ball diameter? Thank you

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Subtracting Two Surfaces (.cube files) for Calculating Fukui Functions
by fsl＠displ.nl 15 Jan '26

15 Jan '26

Hello all, I'm trying to calculate Fukui functions [1] using orca, I'm trying to recreate the plots mentioned in [1] as well. Briefly, I have generated two surface files f_n+1.cube and f_n.cube. I tried running in ChimeraX's console ``` open f_n+1.eldens.cube format cube open f_n.eldens.cube format cube volume subtract #1 #2 ``` But I get is a histogram on side with the level slider, and none of the levels match with the output figure on [1]. I'm not sure how to proceed ahead. Am I missing something, isn't there a surface subtract? rather than volume subtract. The files I used for the plots are in [2]. Regards hisacro. [1]: https://www.faccts.de/docs/orca/5.0/tutorials/react/FUKUI.html [2]: https://displ.nl/pb/lactone2.tar.xz

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Zones help
by Timothy Springer 14 Jan '26

14 Jan '26

I am analyzing a complex made with Alphafold with 7 protein subunits and am trying to find all the interchain contacts. The zone command is useful select zone #1/A 3.6 #1 residues true, but how can I make it find all interchain contacts at once, rather than one chain at a time? What is a command to display sidechains of all residues in the zone? I really like the PAE plot that ChimeraX makes from alphafold predictions. Could I make a similar plot of the contact residues made with the zone command? - 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 New User Inquiry on Superimposing Proteins
by Hsueh, Vincent 12 Jan '26

12 Jan '26

Good morning UCSF ChimeraX Support Team, My name is Vincent Hsueh and I'm a P1 Pharmacy Student at Champan University. I'm a new member to the lab and it seems no one, currently with the lab, has prior experience to using ChimeraX. So far, I have isolated the Human ACE hAChE (PDB: 3LII) in the .csx file attached to the email. My PI gave me the task to superimpose to proteins, Human AChE (PDB: 3LII) colored in Beige and hTg ChEL (PDB 6SCJ) colored in Gold, but I'm having issues learning how to do it on my own. I'm trying to isolate Chain #B from PDB: 3LII with PDB: 6SCJ to see which part of 6SCJ is adjacent to 3LII prior to isolating both chains. I tried reading the ChimeraX user guide, and created the attached "in-progress(super-imposed)_final.csx file, but I'm still not sure how to do it properly. So far, I've opened my isolated PDB: 3LII model in ChimeraX, opened the PDB: 6SCJ file, used the matchmaker command, highlighted the corresponding sequences in SequenceViewer, but my PI has told me that the resulting model still has minor issues. Hopefully, I can gain some guidance in this effort to learn ChimeraX on my own, for my lab, and for future lab members! Vincent Hsueh PharmD Candidate Class of 2028 Chapman University School of Pharmacy vhsueh(a)chapman.edu<mailto:catvu@chapman.edu>

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Determine angle and axis while using Matchmaker
by Sen, Anindito 08 Jan '26

08 Jan '26

Dear All, I have 2 models of a protein positioned in different places in a complex macromolecular assembly. Using Matchmaker I can align the 2 models. How can I get the angles and the axis of rotation/orientation that is calculated to align the 2 models in Matchmaker. Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu<http://microscopy.tamu.edu/>

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how to make a contour plot from Gaussian16 cube file
by Steven Brawer 07 Jan '26

07 Jan '26

I have used Chimerax for proteins, and it is indeed wonderful. However, now I would like to use it to view output from the Gaussian16 "computational chemistry" program, and I am at a loss. I believe the "volume" command is what I need, but I have a LOT of trouble understanding the terminology of the user documentation for the "volume" command. Perhaps someone can be very specific and guide me in the particular procedure described below (or tell me Chimerax does not do such a thing). I have a Gaussian16 cube file for electron density. (This is electron density on grid points. Chimerax can read this file.) I would like to make a contour plot - say contours in the xy plane at z = 0. I would like to specify the number of contours. I would like to know the distance (in au units) of any point on a particular contour from the origin (x=y=z=0) or even from some arbitrary point in space. I would like some sort of legend indicating the density value of each contour. How can I set this up? It would also be nice to be able to specify any plane. Thanks very much Steve

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Measuring contact area in a pdb file
by Shimberg, Geoffrey (NIH/VRC) [C] 07 Jan '26

07 Jan '26

Dear ChimeraX Developers, I was wondering if you could explain to me how to measure the contact residues/area in a pdb file containing an antibody and antigen? I have been trying to do either measure buriedArea or contactArea, but I get an error. I have been using the PDB file 7Y0W as a starter structure to then use for future structures. Let me know if you need anything else. Thank you for all your help. Geoffrey Shimberg

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Surface overlapping with atomic model
by naeshi9min＠postech.ac.kr 07 Jan '26

07 Jan '26

Hi, I'm Gumin Han from South Korea. Thank you for your wonderful visualization tools. This is my first time writing a question here. I want to overlap my models with surface as shown in the link (Figure panel B) https://www.nature.com/articles/s41467-024-49516-2/figures/1 Which options should I use? Thank you for reading my E-mail and best wishes for the New Year' Best regards, 2026, Jan 7th Gumin Han

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Trouble installing ISOLDE in ChimeraX
by Heng Jiang 06 Jan '26

06 Jan '26

Dear ChimeraX Support Team, I hope this message finds you well. I am currently trying to install the ISOLDE plugin in UCSF ChimeraX via Tools → More Tools…, but unfortunately, the installation does not work. I have attempted multiple approaches, but the “More Tools” window does not open. Could you please advise if there is an alternative way to install ISOLDE, such as an offline installation method or by providing the necessary plugin files directly? Thank you very much for your time and assistance. I look forward to your reply. Best regards, Heng Jiang

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Is toolshed down?
by jurkeviciute.gabija＠gmail.com 06 Jan '26

06 Jan '26

Hi, Apologies to bother, but I cannot seem to access toolshed to install isolde on either chimerax 1.11 or my web browser. I checked in with some colleagues and they reported the same thing. Is the site down for the toolshed by any chance? Thanks! Gabija

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Video Tutorial on Protein Interaction Modeling
by David S. Fay 05 Jan '26

05 Jan '26

Hi Everyone, Despite not really being qualified, I’ve done several protein modeling workshops at universities over the past year with some positive responses. It seems to be quite useful to a good number of scientists like myself (clueless molecular/cellular biologists etc), and in particular for less experienced users. Part of my ability to pull this off at any level has been the help I’ve received from others including the wonderful staff the ChimeraX, who I give ample props to in the video. Anyway, feel free to share with students or others who might find this useful. It’s rather long (97 minutes) and I do go into a fair bit of detail about how ipTM is determined along with some of the recently developed alternative metrics for scoring protein-protein interactions. I’ve attached the link below. I also realize that this user group is very sophisticated, so feel free to comment or correct and to add to anything I may have missed or not stated properly. Thanks and happy new year, David David S. Fay Ph.D. Professor, Department of Molecular Biology Director (PD/PI), National Institutes of Health Wyoming INBRE University of Wyoming email: davidfay(a)uwyo.edu<mailto:davidfay@uwyo.edu> <https://youtu.be/u63oYfWDBoM> [maxresdefault.jpg] David's AlphaFold WorkShop 2026<https://youtu.be/u63oYfWDBoM> youtu.be<https://youtu.be/u63oYfWDBoM>

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Boltz affinity prediction
by George Tzotzos 03 Jan '26

03 Jan '26

Happy New Year to all I’m unable to find out how to obtain Boltz binding affinity predictions. Probably, I’m missing out something. Any help would be most welcome. I’m attaching a screenshot for easy diagnostics. Many thanks

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help for RMSD
by marian.vincenzi 23 Dec '25

23 Dec '25

Dear Chimera staff, I am a PostDock from CNR-IBB of Naples (Italy). I am contacting you on the command "match" because I would use it to evaluate rmsd between two structures. I realized (maybe I am wrong) that the value given as output rises from the overlap only on C-alpha, but I used the command "match #1@n,ca,c,o to #2:904-976@n,ca,c,o". My aim was the RMSD evaluated on all backbone atoms and not only c-alpha. Is there anyway to get RMSD value on all backbone atome and overlap the two analysed structures ? Thank you in advance. While waiting, I wish all you team Merry Christmas and Happy New year :-) Marian

2 1

New File Format for Recent ChimeraX Versions
by kkssy141＠gmail.com 22 Dec '25

22 Dec '25

Hello, I recall installing support for the XYZ file format by following the tutorial for older versions of ChimeraX, which worked as expected: https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_read_format… However, in recent ChimeraX versions (1.10 and 1.11), the same procedure no longer works. When running devel install, I encounter the below error message. I was wondering whether the documentation might need to be updated. Thanks. Best, Siyoung ``` devel install /Users/siyoungkim/Downloads/tut_read /Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: Freeware See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#licen… for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py running bdist_wheel installing to build/bdist.macosx-10.9-universal2/wheel running install running install_lib copying build/lib/chimerax/tut_read/io.py -> build/bdist.macosx-10.9-universal2/wheel/./chimerax/tut_read Traceback (most recent call last): File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/devel.py", line 180, in _run unbound_method(bb, *args, **kw) File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/bundle_builder/bundle_builder.py", line 165, in make_install _ = self.make_wheel(debug=debug) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/bundle_builder/bundle_builder.py", line 120, in make_wheel raise RuntimeError(f"Building wheel failed: {wheel}") RuntimeError: Building wheel failed: ChimeraX_TutorialReadFormat-0.1-py3-none-any.whl ```

3 2

Re: ChimeraX Boltz prediction running eternally or failing submission to MSA server
by Arthur Kaser 22 Dec '25

22 Dec '25

Same here. Boltz2 appears to stall at api.colabfold.com<http://api.colabfold.com>, regardless of size/ length of the input sequence. Nil return at this step.

2 2

Assistance with ChimeraX
by Vinita Pant 22 Dec '25

22 Dec '25

Dear ChimeraX Team, I am currently using ChimeraX 1.10.1 (2025-07-24) for preparing my protein for molecular docking, and I would like your guidance on repairing missing side chain atoms. I have explored several resources but have not yet found a solution. I appreciate any assistance you can provide to help me navigate this process effectively. Thank you for your support. *Thanks and Regards* *Vinita Pant* *Doctoral Student (SRF)* *ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal* *Mobile No.: +91 9536940943*

2 4

Installing ChimeraX bundle with none Python file
by huybk81＠gmail.com 21 Dec '25

21 Dec '25

Hi, I am making a ChimeraX bundle. I need to read a csv file as template for the bundle. However, the template file (inside src folder) was not copied or added when installed. Is there anything that I should do to get it copied?

3 2

Read CASTP pocket file
by George Tzotzos 19 Dec '25

19 Dec '25

Hi everybody, I’m following instructions in https://rbvi.github.io/chimerax-recipes/castp/castp.html open 1pn9 readcastp /Users/george/Downloads/1pn9/1pn9.poc and get Unknown command: readcastp /Users/george/Downloads/1pn9/1pn9.poc Any ideas why this is so. Many thanks George

2 1

kvFinder tool
by George Tzotzos 19 Dec '25

19 Dec '25

I’ve opened 1PN9.pdb deleted all but chain A. I used kvfinder #1 probeIn 1.4 probeOut 4.0 The largest cavity has an ID 1.1.5. How does one identify the residues that line the cavity? Thank you

2 2

Request for ChimeraX Installation Assistance
by CykaZH 19 Dec '25

19 Dec '25

Dear ChimeraX Team, I hope this message finds you well. I am writing to seek your assistance regarding the download of the latest version of ChimeraX. Currently, I am located in China, and the download speed for the software is extremely slow, even when using a VPN or an educational network. Additionally, when attempting to download via these methods, I encountered a page requiring a license, which prevented me from completing the download. To ensure a smoother and more efficient setup process, I would like to kindly ask if it would be possible for you to send the latest version of ChimeraX in .exe format as an email attachment. This would greatly help me avoid the download speed issues and the license-related obstacles I am currently facing. Thank you for your time and support. I truly appreciate your assistance and look forward to your response. Best regards, CykaZH Affiliated Hospital of Jiaxing University

2 1

ChimeraX REST remotecontrol: CORS for localhost clients?
by Boris Steipe 18 Dec '25

18 Dec '25

Dear ChimeraX team - I am writing a local, interactive tutorial (Quarto HTML) that I want drive ChimeraX via the REST remotecontrol interface. I can send commands in JavaScript, but not read responses. Quarto serves my page locally - page origin: http://localhost:5779 - ChimeraX endpoint: http://127.0.0.1:61803/run?command=... ... but if I issue in the JS console: fetch("http://127.0.0.1:61803/run?command=help") .then(r => r.text()).then(console.log).catch(console.error); I get: Console error: - CORS blocked: “No ‘Access-Control-Allow-Origin’ header is present…” - Network panel shows 200 OK, but the Fetch promise rejects with TypeError: Failed to fetch. So: Is there a supported way (or could there be) for remotecontrol rest to emit CORS headers for localhost-only clients? Something like: - Access-Control-Allow-Origin: http://localhost:5779 (or a configurable allow-list, possibly including http://127.0.0.1:*) - Access-Control-Allow-Methods: GET, POST, OPTIONS - Access-Control-Allow-Headers: Content-Type - Handling preflight OPTIONS requests (e.g. relevant for POST ) - Even an "allow only loopback origins" mode would be sufficient. Ideally, enabling CORS would be controllable at runtime from within ChimeraX (e.g., as an option to remotecontrol rest start or a subsequent ChimeraX command), so that a teaching workflow can be fully self-contained. For example, something like: • remotecontrol rest start port 61803 cors allow-origin http://localhost:* • or: remotecontrol rest cors allow-origin http://localhost:* If there’s already an option/flag for this I would be grateful for pointers. (Or perhaps I have missed a recommended pattern.) Thank you! Boris (Nb. I do understand the security implications of CORS; this use case is strictly local (loopback only), with the goal to enable processing measurements/queries in browser-based teaching material. ) -- Boris Steipe MD, PhD Professor em. Department of Biochemistry Temerty Faculty of Medicine University of Toronto

2 2

Coloring amino acid residues by type
by Elaine Meng 18 Dec '25

18 Dec '25

Hello, I may not understand your comment, but you can certainly color amino acids specified by residue type. For example, ChimeraX commands: color :asp,glu red color :lys,arg blue color :his dodger blue I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 18, 2025, at 12:13 PM, B. Sharmila Sri <e6123008(a)sriher.edu.in> wrote: > > easy to use, but coloring the aminoacid residues by code is not working properly kindly make it possible > _______________________________________________ > Chimerax-registration mailing list -- chimerax-registration(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-registration-leave(a)cgl.ucsf.edu

1 0

Regarding Internal Server Error while Downloading Chimera X
by Piyush Mohanty 16 Dec '25

16 Dec '25

Dear Administrator, I encountered an Internal Server Error while accessing the server today while downloading the candidate version of ChimeraX. The error message suggested contacting you at root@localhost. The exact error stated was : " Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error. More information about this error may be available in the server error log." Could you please look into this issue and correct the misconfiguration at the earliest convenience? Thank you for your assistance. Best regards, Piyush Mohanty

1 0

Download UCSF ChimeraX Internal Server Error
by Mark Guthridge 16 Dec '25

16 Dec '25

Dear Sir/Madam I am getting an Internal Sever Error when trying to download ChimeraX from https://www.rbvi.ucsf.edu/chimerax/download.html The error message indicates, "contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error." The times of the errors occurred between 4:20pm and 4:30pm AEDT (ie. in the 10min period before I sent this email so you can check logs for my timezone). My IP is 14.2.62.78 The errors occur: * After deleting my cache * In multiple browsers (chrome, firefox, edge) * For multiple releases of ChimeraX spanning 2017-2025 * My local home network and also my phone hotspot * For both ChimeraX and Chimera * Incognito browser Could you please help? Cheers Mark Could you please help A/Professor Mark Guthridge Room L2.09.02 Centre for Cellular and Molecular Biology (CCMB) School of Life & Env. Sciences Deakin University Burwood Highway Burwood VIC 3125 +61 3 924 45796 Important Notice: The contents of this email are intended solely for the named addressee and are confidential; any unauthorised use, reproduction or storage of the contents is expressly prohibited. If you have received this email in error, please delete it and any attachments immediately and advise the sender by return email or telephone. Deakin University does not warrant that this email and any attachments are error or virus free.

2 1

Download Links for ChimeraX 1.11 broken
by Simon Michnowicz 16 Dec '25

16 Dec '25

Dear Group the download links for the latest Chimera on page https://www.rbvi.ucsf.edu/chimerax/download.html#candidate are broken, i..e the following link is broken.. <goog_247633214> https://www.rbvi.ucsf.edu/chimerax/cgi-bin/secure/chimerax-get.py?file=curr… as well as other Unix distros regards *---Simon Michnowicz * Senior Application Specialist, High-Performance Computing *Research Support Services - eSolutions* *Monash eResearch Centre* Monash University 15 Innovation Walk, Building 75, Clayton Campus Wellington Road, VIC 3800 Australia T: +61 3 9902 0794 M: +61 3 0418 302 046 E: simon.michnowicz(a)monash.edu monash.edu

2 1

"Nearby" atoms are within X angstroms of cavity points
by Berenice E Cowfer Chavez 15 Dec '25

15 Dec '25

Hello, What is the default value of "Nearby" atoms are within X angstroms of cavity points in the Find Cavities tool? I remember it used to be 5.0 A but now when I use the tool it shows 6.0 A. Sincerely, Berenice E. Cowfer Chavez, M.S. Lab Manager, Profs. Johnson and Shoulders Labs Massachusetts Institute of Technology

2 2

Adding models as a group/subgroup using Python
by huybk81＠gmail.com 15 Dec '25

15 Dec '25

I tried to read the Programming API but was unable to find out. Right now: I created surface A1,A2,B1,B2,D1,D2, etc.. I added these surfaces in a list surfs = [] surfs.append(A1) surfs.append(A2) ... surfs.append(D2) session.models.add_group(surfs, name="All surface") This make A1,A2 as models #1.1,#1.2 etc Interestingly, I cannot even find the document for add_group. I learned this from ChimeraX recipes. Anyway, I want to organize the data a bit better to have it like this #1; Surface ---> #1.1 Surf A -------> #1.1.1 A1 -------> #1.1.2 A2 ---> #1.2 Surf B -------> #1.2.1 B1 -------> #1.2.2 B1 How can we do that? Best,

2 1

Security Inquiries
by Anh-Huy Le 15 Dec '25

15 Dec '25

Hi ChimeraX folks, I know that this is mostly research software offered through educational channels, but as part of an internal security review of software we are using, I am writing you to inquire if ChimeraX already has any systems in place to report security related issues which could include any of the following: * System breaches on your end that could affect our organization (e.g.: payment information or other types of information being stolen/breached) * Uptime status of services your provide (e.g.: like this Amazon dashboard) * Systems that when queried report the latest updates to combat known security vulnerabilities. If you do not provide these services currently, do you plan on providing these services in the future? If you do not plan on providing these services in the future, would you consider offering professional services to develop these features? Thank you so much for answering ahead of time. Sincerely, Anh-Huy Phan Le, PhD (He/him) Sr. R&D Solution Architect [signature_2852565164]-- Vir Biotechnology, Inc. ale(a)vir.bio<mailto:ale@vir.bio> | Mobile: 714-269-9663 --

2 1

bug report - pip list failure
by replacement2＠gmail.com 15 Dec '25

15 Dec '25

Hi, My apologies if this is not the best place to report a bug. There appears to be an issue with `pip list`, which may be caused by a typo in `pip.py`. Please see the traceback. It'd be great if someone can verify. Thanks. Traceback (most recent call last): File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute cmd.run(cmd_text) File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/pip.py", line 71, in pip pip_cmd.appendf("list") ^^^^^^^^^^^^^^^ AttributeError: 'list' object has no attribute 'appendf' cui5

4 4

ChimeraX Boltz prediction running eternally
by Sam Allen 10 Dec '25

10 Dec '25

Hello Tom and co., I am currently trying to use ChimeraX Boltz tool to predict the structure of some small ligands onto a GPCR and my prediction running timer just never stops. I initially attempted to install and run the tool on Windows but the install failed to import the mols folder properly multiple times (uninstall and reinstalled), after manually untaring the folder in Powershell it still didn't run (Timeout while submitting to MSA server). I then decided to switch over to my mac (M1 16GB) and while the install of Boltz in ChimeraX no longer had any error and the prediction didn't error either, the timer just continued to go up (to 26000 eventually). I figured the protein was too large (471 residues, makes sense), so I tried to rerun one of your test examples (8rf4, https://www.rbvi.ucsf.edu/chimerax/data/boltz-apr2025/runtimes.html) and still no prediction output after 20 minutes. I've tried switching from default compute device to GPU or CPU and still no difference. Additionally, in activity monitor it shows ChimeraX is taking up nearly no GPU or CPU usage, so I'm confused as to what is happening. Do you have any advice or know anything that might be going wrong that I can fix? Regards, Sam

2 1

ChimeraX Boltz prediction running eternally or failing submission to MSA server
by Sam Allen 10 Dec '25

10 Dec '25

Hello, I am currently trying to use ChimeraX Boltz tool to predict the structure of some small ligands onto a GPCR and my prediction running timer just never stops. I initially attempted to install and run the tool on Windows but the install failed to import the mols folder properly multiple times (uninstall and reinstalled), after manually untaring the folder in Powershell it still didn’t run (Timeout while submitting to MSA server). I then decided to switch over to my mac (M1 16GB) and while the install of Boltz in ChimeraX no longer had any error and the prediction didn’t error either, the timer just continued to go up (to 26000 eventually). I figured the protein was too large (471 residues, makes sense), so I tried to rerun one of your test examples (8rf4, https://www.rbvi.ucsf.edu/chimerax/data/boltz-apr2025/runtimes.html) and still no prediction output after 20 minutes. I’ve tried switching from default compute device to GPU or CPU and still no difference. Additionally, in activity monitor it shows ChimeraX is taking up nearly no GPU or CPU usage, so I’m confused as to what is happening. Do you have any advice or know anything that might be going wrong that I can fix? Update: After this email I downloaded the daily ChimeraX version and attempted to run Boltz through that. Instead now the same error as the windows appeared (No authentication provided for MSA server; Failed to process; Skipping. Error: Too many failed attempts for the MSA generation request..) Below is the error in its entirety: Running boltz prediction failed with exit code 0: command: /Users/samuelallen/boltz22/bin/boltz predict /Users/samuelallen/Desktop/boltz_testingtesting123/testingtesting123.yaml --use_msa_server --accelerator gpu --no_kernels stdout: Boltz version 2.2.0 MSA server enabled: https://api.colabfold.com MSA server authentication: no credentials provided Checking input data. Processing 1 inputs with 1 threads. Generating MSA for /Users/samuelallen/Desktop/boltz_testingtesting123/testingtesting123.yaml with 1 protein entities. Calling MSA server for target testingtesting123 with 1 sequences MSA server URL: https://api.colabfold.com MSA pairing strategy: greedy No authentication provided for MSA server Failed to process /Users/samuelallen/Desktop/boltz_testingtesting123/testingtesting123.yaml. Skipping. Error: Too many failed attempts for the MSA generation request.. stderr: 0%| | 0/1 [00:00<?, ?it/s] 0%| | 0/150 [elapsed: 00:00 remaining: ?][A SUBMIT: 0%| | 0/150 [elapsed: 00:00 remaining: ?][AError while fetching result from MSA server. Retrying... (1/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (2/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (3/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (4/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (5/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (6/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) SUBMIT: 0%| | 0/150 [elapsed: 01:04 remaining: ?] Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 534, in _make_request response = conn.getresponse() ^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connection.py", line 571, in getresponse httplib_response = super().getresponse() ^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1395, in getresponse response.begin() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 325, in begin version, status, reason = self._read_status() ^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 286, in _read_status line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py", line 706, in readinto return self._sock.recv_into(b) ^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1314, in recv_into return self.read(nbytes, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1166, in read return self._sslobj.read(len, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TimeoutError: The read operation timed out The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/adapters.py", line 667, in send resp = conn.urlopen( ^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 841, in urlopen retries = retries.increment( ^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/util/retry.py", line 474, in increment raise reraise(type(error), error, _stacktrace) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/util/util.py", line 39, in reraise raise value File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 787, in urlopen response = self._make_request( ^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 536, in _make_request self._raise_timeout(err=e, url=url, timeout_value=read_timeout) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 367, in _raise_timeout raise ReadTimeoutError( urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/data/msa/mmseqs2.py", line 77, in submit res = requests.post( ^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/api.py", line 115, in post return request("post", url, data=data, json=json, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/api.py", line 59, in request return session.request(method=method, url=url, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/sessions.py", line 589, in request resp = self.send(prep, **send_kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/sessions.py", line 703, in send r = adapter.send(request, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/adapters.py", line 713, in send raise ReadTimeout(e, request=request) requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/main.py", line 581, in process_input compute_msa( File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/main.py", line 477, in compute_msa unpaired_msa = run_mmseqs2( ^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/data/msa/mmseqs2.py", line 201, in run_mmseqs2 out = submit(seqs_unique, mode, N) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/data/msa/mmseqs2.py", line 92, in submit raise Exception( Exception: Too many failed attempts for the MSA generation request. 100%|██████████| 1/1 [01:04<00:00, 64.69s/it] 100%|██████████| 1/1 [01:04<00:00, 64.69s/it] GPU available: True (mps), used: True TPU available: False, using: 0 TPU cores HPU available: False, using: 0 HPUs /Users/samuelallen/boltz22/lib/python3.11/site-packages/pytorch_lightning/trainer/connectors/logger_connector/logger_connector.py:76: Starting from v1.9.0, `tensorboardX` has been removed as a dependency of the `pytorch_lightning` package, due to potential conflicts with other packages in the ML ecosystem. For this reason, `logger=True` will use `CSVLogger` as the default logger, unless the `tensorboard` or `tensorboardX` packages are found. Please `pip install lightning[extra]` or one of them to enable TensorBoard support by default Regards, Sam

1 0

Boltz run- Kd values
by Malik, Radhika 08 Dec '25

08 Dec '25

Hello, I am a Research Scientist at Mount Sinai School of Medicine, NY. I have run Boltz in ChimeraX on a protein-ligand complex, however, I am not able to locate the file for the predicted Kd values. Can you please direct me to the file/location? I am attaching a screenshot of what I see after the run. Thanks a lot, Radhika ________________________________ Confidentiality Notice: This electronic mail transmission and any documents, files, or previous email messages attached to it may contain confidential information and are intended solely for the use of the individual or entity to which they are addressed. If you are not the intended recipient, or a person responsible for delivering such information to the intended recipient, you are hereby notified that any further review, disclosure, copying, dissemination, distribution, or use of any of the information contained in or attached to this email transmission is strictly prohibited. If you have received this message in error, please notify the sender immediately by email, discard any paper copies, and delete all electronic files of the message. Thank you for your cooperation.

4 9

NEED HELP TO INSTALL BOLTZ2 in CHIMERAX.
by Dr. V.N. Balaji 07 Dec '25

07 Dec '25

Subject: Bug Report: "Intel Mac" Error Blocking Boltz Install on Windows 11 (NVIDIA 3080 Ti) Dear ChimeraX Team, I am writing to report a platform detection bug in the Boltz installer within ChimeraX (Daily Build 1.12.dev202512040236). When attempting to install Boltz via the boltz install command on a Windows 11 system with a compatible NVIDIA GPU, the installation fails immediately with the following error: "Boltz requires newer Torch versions that are not available on Intel Macs." This appears to be a false positive in the installer's logic, erroneously flagging my Windows/x86_64 system as an unsupported Intel Mac. System Configuration: OS: Windows 11 Pro (x86_64) CPU: Intel Core i9-7940X GPU: NVIDIA GeForce RTX 3080 Ti (12GB VRAM, CUDA 12.x active) ChimeraX Version: 1.12.dev202512040236 (2025-12-04) Context & Troubleshooting: Verified Hardware: I have already successfully installed and verified boltz (v2.2.1) in a standalone PowerShell environment on this same machine; it runs protein-ligand docking with GPU acceleration without issue. Workarounds Attempted: I have tried running ChimeraX in admin mode, using different daily builds, and attempting to manually intervene with pip, but the internal installer aborts before package retrieval begins due to this platform check. Request: Could you advise on a command-line flag or manual workaround to bypass this platform check and force a Windows/CUDA installation? Alternatively, if this requires a patch to the installer script to correctly identify Windows environments, please let me know. Thank you for your assistance. Best regards, V.N. Balaji, Ph.D. Computational Chemist Bangalore, India vnbalaji(a)gmail.com | LinkedIn: vnbalaji

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Can ISOLDE-refined models be directly deposited to the PDB?
by man6ny＠virginia.edu 05 Dec '25

05 Dec '25

Dear all, Maybe an ignorant or previously-asked question... I believe most people refine cryo-EM models using e.g. Phenix real-space-refine before depositing them to the PDB. Is there a strict reason (practical or philosophical) why cryo-EM models refined in ISOLDE cannot be directly deposited without subsequent refinement in Phenix or Refmac? I have a high-resolution map (2.2 A) but the latter programs seem to actually make my model worse (e.g. Phenix tends to give me rotamers that are not supported by the experimental data). I would prefer to use the model refined in ISOLDE but perhaps I am missing something? Many thanks for your insight! Louis

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Opening multiple chimeraX windows at the same time?
by Choy, Jon 05 Dec '25

05 Dec '25

Hi Oliver and Tom or whom it may concern, I was interested in whether it is possible to open multiple .cxs files at the same time? I am comparing structural features across many different proteins and their corresponding maps—and it is very annoying to be only able to open one map and its protein at a time. Although it is possible to load multiple resolved structures and their maps into a single .cxs file, these structures all load onto different spots on the chimeraX interactive space—making side by side comparison a bit cumbersome. Assistance in this would be massively appreciated! Thank you so much and looking forward to hearing from you. Best, Jon

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Calcium ions labeled as solvent, not as ions
by Ute Roehrig 05 Dec '25

05 Dec '25

Hello, I am not sure if this is a problem in the structure or in ChimeraX or intentional, but I remarked that in PDB structure 7tba the calcium ions are labeled as "solvent" and not as "ions", although the element and atom type seem to be OK. I did not see the same in other PDB structures with calcium. Thank you for your help, Ute

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