- ChimeraX-users - RBVI Mailing Lists

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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questions for ChimeraX
by Jéromine Carret 21 Oct '25

21 Oct '25

Hello, My name is Jéromine, and I am a PhD student at the University of Lille, France. We are working on structural modelling of different protein variants. We have questions about the ChimeraX software tools. We would like to obtain electrostatic maps of protein structures and avoid using the colour scale in order to obtain numerical results. And also for hydrophobicity maps. We also want to study the clashes between the positions of variants. Do you have any advice? For the matchmaker command, can you give me the information I need to understand the results? Thank you in advance for your reply. Kind regards. Jéromine Carret PhD candidate RADEME lab ULR 7364 Université de Lille

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chimeraX daily built, 2025 Oct 20, boltz-2 empty sequence line in yaml file
by Guenter Fritz 20 Oct '25

20 Oct '25

Dear ChimeraX developers, really a great job implementing boltz into chimeraX !! I have just installed the latest daily build 2025 Oct 20 on a Redhat 8 (Rocky 8 derivative) machine. Boltz-2 installs with no visible problem via chimeraX (like before). When I try to run predictions, I get an error which seems to be due to an almost empty yaml file created by chimeraX. Only the first line ("version 1.0") is in the yaml file. Boltz (of course) fails. There should be no problem with permissions. I just installed also the latest release of chimeraX and boltz-1 via chimeraX. Runs as expected. PS: I had no try yet on my mac (will check later). Best wishes, Guenter

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Problems adjusting the phi/psi angles with ChimeraX
by Gong, Zhen 15 Oct '25

15 Oct '25

Dear ChimeraX team, I was trying to use ChimeraX to change the phi/psi angles of a residue in the loop region but encoured this error: ILE 411 N ↔ CA is part of a ring/cycle and cannot be rotated. There is no ring/cycle in ILE411 or neibouring residues: ASN 410 or THR 412. I tried ChimeraX daily (version 1.10.dev202504260127 (2025-04-26) and ChimeraX 1.10.1 but the same error happened. I am wondering if it is possible to change the phi/psi angles with ChimeraX. Thank you. Best, Zhen

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Chimera and ChimerX issues after update to MacOS Tahoe
by Rechiche, Othman 14 Oct '25

14 Oct '25

Hi everyone, I recently updated to MacOS Tahoe, Since then I encountered several issues with Chimera, ChmieraX and python. I installed and removed and reinstalled the apps but I still get the same error. For chimera I get this error: [Screenshot 2025-09-24 at 12.08.51 AM.png] FOr ChimeraX, when I try to open a session, it complains that the session was created with another version of python. I opened that session successfully several times before to the update of MacOS and I have never seen this error before. Failed opening file /Users/x/x/x/x/x/x/x/x.pyc: Python code was compiled for a different version of Python Can you please help me fix this? Best Regards, Othman Dr. Othman Rechiche Herbert Irving Comprehensive Cancer Center Columbia University Medical Center Columbia University New York, NY 10032 email: or2296(a)cumc.columbia.edu phone: +1 (814) 880-5554

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