July 2026 - ChimeraX-users - RBVI Mailing Lists

MCP for ChimeraX
by Alexis Rohou 20 Oct '26

20 Oct '26

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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Change default molecule display to cartoon only (hide atoms)
by ramy.kazan＠ibpc.fr 18 Aug '26

18 Aug '26

Hi all, When I open a large model (e.g., a ribosome) in ChimeraX, the default display style shows it as atoms in the spheres style. I’d like to change this so that, by default, all atoms are hidden, and the model is displayed as a cartoon only. I’ve created an alias with the necessary commands and mapped it to a function key for quick adjustments. However, this approach has a limitation: after customizing one model (e.g., showing specific residues as atoms), opening a new model and using the function key overwrites the customized residues, applying the "cartoon-only" style to all open models. There must be a setting to adjust this behavior, but I haven’t been able to find it. I also recall reading that ChimeraX treats small and large models differently—perhaps based on the number of chains or residues—but I can’t remember the exact rules. Could someone point me to the correct way to set this as the default behavior for all new molecules? Thanks for your help! Best regards, Ramy

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clip
by Timothy Springer 10 Aug '26

10 Aug '26

Can you translate this into a clip command I can use in a .cxc file? clip list Using 2 clip planes: near offset -3.0783, axis -0.462,-0.880,0.109, point on plane 218.1,184.5,202.4) far offset 12.676, axis 0.462,0.880,-0.109, point on plane 210.8,170.6,204.1) - 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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cartoon style setting
by junjie han 07 Aug '26

07 Aug '26

Hi, May I ask how I can set the cartoon thick for a specific region of a structure in ChimeraX? For instance, the command "cartoon style #1/A:10-20 thick" plays an effect on the whole #1 molecule, not only affecting the specific region #1/A:10-20. Please let me know what the appropriate command is by any chance. Thanks, Junjie

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select by atom type in given model
by Steven Brawer 31 Jul '26

31 Jul '26

I have three models of the same protein. How can I select C3 carbons in a given model? When I do sel #3 C3 I get an error "Expected a Keyword". Therefore I have to select C3 in ALL models sel C3 and then do ~sel #1,2 for example, which deselects in models 1, 2. If I do "sel C3" and ctrl-click "in" model 1(only model 1 is visible), say, it deselects in all models. Is there a way to just select all C3 in model 3 in one single command? Is there a "keyword" for atom type (analogous to @ for atom names)? This would be very useful, for example, in command (cxc) files, where I wouldn't have to delineate all the models. (I suppose I could do ~sel #1,2,4,5,6,7,8 in a command file. This is ugly.) Thanks Steve

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cannot hide/delete hydrogens once added to protein
by Steven Brawer 28 Jul '26

28 Jul '26

Newbie: I ran open 2zcp delete /B delete solvent hide cartoons show atoms addh #1 hbond false ----------- lots of H atoms, colored white by default color @HC pink ------ NOTHING HAPPENS hide @HC --------- NOTHING HAPPENS hide #1 @HC --------- NOTHING HAPPENS select @HC --------- NOTHING HAPPENS select #1 @HC --------- NOTHING HAPPENS delete #1 @H ------ does not work either. How can I hide or delete the hydrogens? My understanding (from the documentation) is that HC denotes hydrogens bonded to carbons, H denotes hydrogens bonded to N or O (as appropriate) The following DOES work (sanity check) select C3 delete sel Thanks Steve

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ChimeraX crashed immediately when it tried to display hydrogen bonds.
by 2326313726＠qq.com 28 Jul '26

28 Jul '26

The Windows system I'm using. When I open a pdb file and want to display the hydrogen bonds near this residue, the software immediately shuts down. This issue didn't exist a week ago. I uninstalled and reinstalled the software today, and also turned off the antivirus software, but still, I can't display the hydrogen bonds.

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ChimeraX crashed immediately when it tried to display hydrogen bonds.
by ？ 27 Jul '26

27 Jul '26

Dear Engineer: The Windows system I'm using. When I open a pdb file and want to display the hydrogen bonds near this residue, the software immediately shuts down. This issue didn't exist a week ago. I uninstalled and reinstalled the software today, and also turned off the antivirus softchimerax-users(a)cgl.ucsf.eduware, but still, I can't display the hydrogen bonds. Thank you very much. Wishing you a happy life. ？ 2326313726(a)qq.com

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removing MMTF support
by Greg Couch 27 Jul '26

27 Jul '26

FYI, unless someone speaks up, we are planning to remove support for MMTF files in ChimeraX 1.13. And that is because two years ago (July 2024) the PDB stopped keeping their repository of MMTF files up-to-date. -- Greg

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Accelerate opening of AlphaFold models with ligands lacking a mmcif template?
by Ute Roehrig 27 Jul '26

27 Jul '26

Dear All, I am often opening AlphaFold 3 co-folding structures including small molecules in ChimeraX. In these models, ligands were provided as SMILES and are called LIG_X (with X being the chain label) in the AF3 output model.cif file. Opening these structures is very slow on my machine, because ChimeraX searches for a template for the ligands and finally fails with the warning "Unable to fetch template for 'LIG_X': will connect using distance criteria". Is there any workaround? E.g. by telling ChimeraX not to look for a template? Thank you for your help, Ute

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