About MCPymol
MCPymol is an MCP server in the Healthcare category: mcp server for pymol for conversational protein display.
Install
git clone https://github.com/chemrich/MCPymolThis server has no ConduID identity, so agent calls to it are not receipted. Pin the version you install and review the source before granting it credentials.
Tools (19)
Can I keep this scene?`save_session` / `load_session`
Parameters not published.
Can I open my own file rather than a PDB code?`load_structure`
Parameters not published.
Can I print it?`print_ribbon_view` + `print_export`
Parameters not published.
Can I see the density around this ligand?`load_map`, then `density_view`
Parameters not published.
How big is this interface, and which residues matter?`interface_report`, then `interface_view`
Parameters not published.
How far apart / what angle / how much surface?`distance`, `angle`, `dihedral`, `sasa`, `rms_cur`
Parameters not published.
How good is this cryo-EM model, per residue?`qscore_view`
Parameters not published.
How much do the members of this ensemble disagree?`ensemble_spread_view`, then `morph_states` if they share a topology
Parameters not published.
Is this atom really there, or is it half-occupied?`occupancy_view`, `altloc_view`
Parameters not published.
What *is* this structure — resolution, method, organism?`structure_info`
Parameters not published.
Show all 19 tools
What are this atom's occupancy / altloc / B-factor?`atom_properties`
Parameters not published.
What does it look like?`render` — returns the image, so the model can see it
Parameters not published.
What holds this ligand in its pocket, and how tightly?`contact_report`, then `ligand_view` to see it
Parameters not published.
What's loaded / what chains / what ligands?`list_objects`, `list_chains`, `list_ligands`
Parameters not published.
What's the sequence, and how does it map to the residue numbering?`get_sequence`
Parameters not published.
What's the voxel size / geometry of this map?`map_info` — reads the header only
Parameters not published.
Where do these two structures differ?`superposition_view`
Parameters not published.
Which parts are conserved? Flexible? Confident?`conservation_view`, `bfactor_view`, `plddt_view`
Parameters not published.
Which parts of this map are actually well resolved?`local_resolution_view`
Parameters not published.
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