- ChimeraX-users - RBVI Mailing Lists

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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help on color command
by James Raymond 12 Oct '25

12 Oct '25

Dear ChimeraX, I have tried 100 variations of color command without success. Can you tell me the command to color residues 132-145 red in this single chain protein? thank you Jim [image: image.png]

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Issue with combining two pdb models in chimeraX
by Rayees Mattoo 10 Oct '25

10 Oct '25

Hi, I have two models #1 Model1.pdb and #2 Model2.pdb having one shared polypeptide, same chain ID but different residue numbers. I wanted to combine them to make a merged_model #3. I used the following combine commandline in chimeraX: combine #1 #2 close false modelId #3 retainIds true name merged_model The resulting combined model appeared to be correct, and I proceeded to run phenix.real_space_refine without any issues. However, when I attempted to deposit the refined model (either in .pdb or .cif format) with the wwPDB, I received a file with multiple errors (see attached). Interestingly, I had previously deposited the individual models (#1 and #2) without any problems. This situation raises my concern about whether the combination process was successful. Is there anything I should have done differently to ensure a seamless combination of the models? Best Rayees

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ChimeraX-1.10.1 syntax issue
by wwvivian.wang＠mail.utoronto.ca 10 Oct '25

10 Oct '25

Hi, this is my first time using ChimeraX-1.10.1 and I ran into a little bit of trouble with syntax errors in this version.\ I opened a pdb file that contains two chains of proteins that I'm interested in - Chain A and B. I then renamed and coloured them to Chain C and D for clarity. In the Contacts window, I made the following changes: Find pairs of atoms with: ✅ VDW overlap ≥ –0.4 Å Limit by selection: ✅ with at least one end selected Ignore interactions between atoms 4 or fewer bonds apart: ✅ Ignore interactions between residues <5 apart: ✅ Include intermodel: ✅ Include intramodel: ❌ (uncheck it) Include intramolecule: ❌ (uncheck it) Ignore hidden models: ✅ Display as pseudobonds: ✅ (keep green, radius 0.075, dashes 6) Write info to: Log ✅ Then click Apply I then selected the atomic model #1 (Chain C+D) and deselected surface models #1.1 (Chain C) and #1.2 (Chain D) and ran the Contacts Command: "contacts atoms #1/C #1/D makePseudobonds true distanceCutoff 4.0 log true" but the software returns "Expected a keyword" argument and highlighted "distanceCutoff 4.0 log true" in red. Alternatively, I also tried "findclash #1/C test #1/D overlapCutoff -0.4 hbondAllowance 0 interModel true intraMol false intraRes false makePseudobonds true select true log true" but again it fails to output contact coordinates between the two chains and returns the following: "Unknown command: findclash #1/C test #1/D overlapCutoff -0.4 hbondAllowance 0 interModel true intraMol false intraRes false makePseudobonds true select true log true". I would appreciate your help in resolving this error for me. Thanks, Vivian

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Focus in ChimeraX
by Luca Pellegrini 10 Oct '25

10 Oct '25

Hi, What is the ChimeraX equivalent to the Focus command in Chimera? I have selected a portion of a structure, and would like to bring it into focus without dragging it into view. Also Focus would automatically set the selection as the pivot point. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA lp212(a)cam.ac.uk

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Question about using ChimeraX
by 张圃源 09 Oct '25

09 Oct '25

Hi， I'm a new user of ChimeraX and I'm currently facing a problem. I want to convert a pdb file into an mrc file that can be input into cryoSPARC, and this mrc file should be in the form of a cube volume. I will use ChimeraX to achieve this. How should I proceed? Best Yuan 中山大学张圃源

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tools for ligand-receptor interactions
by Elaine Meng 09 Oct '25

09 Oct '25

> On Oct 8, 2025, at 9:58 AM, Vojo P Deretic <VDeretic(a)salud.unm.edu> wrote: > > Hi > How do I pose a question - via email or on the site? > My question is: we have a Boltz/alphafold fitted organic molecule into a known structure. > What are the tools for residue interactions in ChimeraX apart from H bonding and hydrophobic or charged surfaces? > Thanks > Vojo Deretic > Hi Vojo, As per the Contact Us page <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html> ...to ask questions you would use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address, which is CC'd here so you don't need to send your questions again. I don't know what you mean by "on the site" since there is no webform for questions, only this email address. You already mentioned H-Bonds and coloring the receptor molecular surface by ESP (electrostatics) or MLP (lipophilicity). That's most of it. Certainly you can just visually evaluate what is nearby, but you could use the Contacts tool for a more objective approach: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> See also the tutorial "Protein-Ligand Binding Sites" <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> I hope this helps, 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 > On Oct 8, 2025, at 9:58 AM, Vojo P Deretic <VDeretic(a)salud.unm.edu> wrote: > > Hi > How do I pose a question - via email or on the site? > My question is: we have a Boltz/alphafold fitted organic molecule into a known structure. > What are the tools for residue interactions in ChimeraX apart from H bonding and hydrophobic or charged surfaces? > Thanks > Vojo Deretic > > Sent from my iPhone with lots of typos and autocorrect nonsense - my apologies... >

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