- ChimeraX-users - RBVI Mailing Lists

Help with Chain ID commands
by Emily Cioppa 29 Oct '25

29 Oct '25

Good evening, I have a quick question regarding the changechains command in Chimera/ChimeraX. If I have a single model open that inherently has one single chain, is there a way to select a continuous strand of residues in the sequence and change the Chain ID of only the selected residues to something else? It seemed from my online research that this is possible, however, I cannot get it to work. Any advice would be appreciated as soon as possible. Thank you. Best, Emily Cioppa Research Assistant The Rockefeller University

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Average attribute
by Reza Khayat 29 Oct '25

29 Oct '25

Hi, How do I average atom attributes to residue attributes? Let's assume the attributes name is mapvalues. Thanks. Best wishes, Reza Reza Khayat, PhD City College of New York Department of Chemistry and Biochemistry

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Align x,y,z axis of Proteins
by Hübbers, Jan 29 Oct '25

29 Oct '25

Hey support, I have defined x, y, z symmetry axis for a protein complex by forcing axis through centroids of the different subunits. I also created x, y ,z axis that meet at the origin of my scene. Is it possible to align the protein axis to the scene axis? Best, Jan ________________________________________________________________ Dr. rer. nat. Jan W. Hübbers Postdoctoral researcher RWTH Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology Assistant Features Editor The Plant Cell, American Society of Plant Biologists Worringerweg 1, 52074 Aachen, Germany +49 (0)241 80 28130 http://www.bio1.rwth-aachen.de/PlantMolCellBiology/index.html<https://urldefense.com/v3/__http:/www.bio1.rwth-aachen.de/PlantMolCellBiolo…> “The greatest value of a picture is when it forces us to notice what we never expected to see.” John W. Tukey

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ChimeraX pre-built tar package
by Elaine Meng 28 Oct '25

28 Oct '25

> On Oct 22, 2025, at 3:57 PM, Charitha Belluru Shetty via Chimera <chimera(a)cgl.ucsf.edu> wrote: > > Hi Team, > We have the license for ChimeraX in name of Jim Thorpe. Would it be possible to provide the pre-built tar package of the latest version for Redhat 9. > With the previous version we were able to download the pre-build tar package from your website (example: ChimeraX-0.93.tar.gz), but now I see there is only .rpm package (https://www.rbvi.ucsf.edu/chimerax/download.html ) which will need to be installed in the OS level. I was looking to get a pre-build tar file for the latest version so we can install it without having to do the rpm install. I am aware there is github source for ChimeraX where we can build but would greatly appreciate if you could provide tar installer. Thank you! > $ cat /etc/redhat-release > Red Hat Enterprise Linux release 9.4 (Plow) > Best Regards, > Charitha Shetty Hello Charitha Shetty, ChimeraX usage & support questions should be sent to chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (without any data that should be kept private) since the commercial licensing team cannot answer that type of thing. I've CCd that address so you don't need to send your question again. I don't see that as an option on our download page, so my guess is probably not, but we can see if others on the list respond. Regards, 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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Problems with script
by George Tzotzos 28 Oct '25

28 Oct '25

I’d be grateful for your help My script is: # Auto-generated by make_chimerax_assets.py # Visualize L1 composition divergence on delta (1PN9) and epsilon (2IMI) open viz/delta_1PN9.pdb open viz/epsilon_2IMI.pdb defattr viz/delta_div.defattr model #1 defattr viz/epsilon_div.defattr model #2 style #1,#2 cartoon cartoon smoothRibbon true color byattribute divergence palette bluesred range 0,1 #1 color byattribute divergence palette bluesred range 0,1 #2 key colorbar palette bluesred range 0,1 label "Δ composition (L1)" pos 0.85,0.15 size 0.03,0.5 lighting soft zoom true When I try to open the color_delta_epsilon_divergence.cxs (see above), I get: RuntimeError: Not a ChimeraX session file File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 798, in restore raise RuntimeError("Not a ChimeraX session file”) Thank you

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MCP for ChimeraX
by Alexis Rohou 27 Oct '25

27 Oct '25

Hi all, I would like to use ChimeraX via an agent. Quick googling suggests I'm not the first person to think of this (here <https://github.com/chatmol/molecule-mcp>, here <https://github.com/GDAmitha/chimerax-alphafold-mcp>), but before I dive in I thought I'd check - anyone else actively working on this? Or maybe you have worked on it and hit a roadblock? Cheers, Alexis

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Problem with Boltz-2
by Dr. Oscar Perez 23 Oct '25

23 Oct '25

Hello ChimeraX Support, I am trying to use Boltz within ChimeraX to analyze ligand binding affinity, but I cannot find the corresponding option. I do not see any menu item or text that says “Predict Binding Affinity for.” [cid:51284bde-0c95-4cd2-bdd4-9570eef8bf69] When I run an example similar to the one shown in your video for the HIV protease<https://www.youtube.com/watch?v=h06yOBcaOqc> to evaluate ligand interactions, I obtain the generated 3D structure, but no table with ligand prediction values is produced. I installed ChimeraX just yesterday, so I assume I am using the latest version. Boltz is installed inside ChimeraX as well. Could you please advise how I can obtain the ligand interaction values? Thank you, Oscar Oscar Perez-Leal, MD Associate Professor Moulder Center For Drug Discovery Research Temple University School of Pharmacy 3307 N Broad St, Room 556 Philadelphia, PA, 19140 Tel: 215-707-4871 [cid:e222d198-ed2f-42a9-91a3-dab997f1387c]<https://outlook.office.com/bookwithme/user/3647ce5c96e849969435512aaf86933a…> Book time to meet with me<https://outlook.office.com/bookwithme/user/3647ce5c96e849969435512aaf86933a…>

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Question about density map visualization for figures using ChimeraX
by Abhipsa Shatarupa 23 Oct '25

23 Oct '25

Hello, I am currently preparing figures for a publication and am using ChimeraX to render a density map. The color of the mesh representation I am using is set to *licorice*, but after I save the image in TIFF/PNG format at 7602 × 5680 resolution, the mesh appears quite faint. Could you please advise on how to make the density appear darker or more prominent in the saved image? Thank you! -Abhipsa

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Building ions using ISOLDE
by Przemyslaw Dutka 22 Oct '25

22 Oct '25

Hello, I am currently encountering an issue while trying to build Na ions with ISOLDE. Despite various attempts, the ions consistently move outside the density as soon as the simulation begins. The ion site is clearly defined by previous crystallography maps. I have also downloaded several EM maps that include modeled Na ions, such as PDB 6VWX (see below). In these cases, the ion still moves up or down the channel once the simulation starts. The only method I've found to keep the ion in place is by pinning it. I would greatly appreciate any advice or tips. [image: Screenshot 2025-10-21 at 10.33.05 PM.png] Best, Przemek

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building on macOS
by Alexis Rohou 21 Oct '25

21 Oct '25

Hello, I'd like to build from source in order to play with (and possibly hack at) the MCP server. I am on macOS 14.7.6 with Xcode 16.2. I think the compilation went well, but at link time I get warnings and an error. Below is the end of the output of `make install`. What do you recommend I try? Cheers, Alexis available bundle cache has not been initialized yet Executing: devel install . user false exit true noDeps true ld: warning: object file (/Users/rohoua/work/git/ChimeraX/src/bundles/atomic_lib/atomic_cpp/pyinstance_cpp/PythonInstance.o) was built for newer 'macOS' version (11.0) than being linked (10.9) ld: warning: object file (/Users/rohoua/work/git/ChimeraX/src/bundles/atomic_lib/atomic_cpp/element_cpp/Element.o) was built for newer 'macOS' version (11.0) than being linked (10.9) ar: src/lib/libatomstruct_tmpl.a is a fat file (use libtool(1) or lipo(1) and ar(1) on it) ar: src/lib/libatomstruct_tmpl.a: Inappropriate file type or format Traceback (most recent call last): File "/Users/rohoua/work/git/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/_distutils/spawn.py", line 87, in spawn subprocess.check_call(cmd, env=_inject_macos_ver(env)) File "/Users/rohoua/work/git/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py", line 413, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/usr/bin/xcrun', 'ar', 'rcs', 'src/lib/libatomstruct_tmpl.a', 'atomic_cpp/atomstruct_cpp/tmpl/Atom.o', 'atomic_cpp/atomstruct_cpp/tmpl/Bond.o', 'atomic_cpp/atomstruct_cpp/tmpl/CoordSet.o', 'atomic_cpp/atomstruct_cpp/tmpl/Molecule.o', 'atomic_cpp/atomstruct_cpp/tmpl/Residue.o', 'atomic_cpp/atomstruct_cpp/tmpl/TemplateCache.o', 'atomic_cpp/atomstruct_cpp/tmpl/amino.o', 'atomic_cpp/atomstruct_cpp/tmpl/camino.o', 'atomic_cpp/atomstruct_cpp/tmpl/findres.o', 'atomic_cpp/atomstruct_cpp/tmpl/general.o', 'atomic_cpp/atomstruct_cpp/tmpl/ions.o', 'atomic_cpp/atomstruct_cpp/tmpl/namino.o', 'atomic_cpp/atomstruct_cpp/tmpl/nucleic.o']' returned non-zero exit status 1.

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