Many thanks Elaine. Much appreciated.
On 8 Oct 2025, at 17:00, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi George, Both the ideas make sense. It depends how similar the proteins are; if they are similar enough to superimpose well and you just want to get a general idea of the surrounding residues, your superposition method may be enough.
The second idea is to try to build a complex with Boltz, which can be using current ChimeraX (1.10 or newer), but if the ligand is a small organic molecule you have to figure out how to specify it in the input dialog as a SMILES string or PDB residue name (e.g., HEM for heme). You cannot specify the ligand model directly because Boltz requires the other kinds of input instead. See <https://rbvi.ucsf.edu/chimerax/docs/user/tools/boltz.html>
If the ligand is a protein or nucleic acid, you can specify those more directly as structure chains already open in ChimeraX, as described in the help link above.
If you also want a Boltz prediction of ligand affinity (not just binding location) you would have to use a ChimeraX daily build from July 22, 2025 or newer. See <https://www.rbvi.ucsf.edu/chimerax/data/boltz-apr2025/boltz_help.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 5:43 AM, George Tzotzos via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I’m dealing with two structurally similar proteins, one of which is in complex with a ligand (pdb1). The second protein is in the apo-form (pdb2). I’ve used matchmaker to superimpose the structures. Does it make sense to append the ligand coordinates to pdb2? I’m interested to find out which residues lie within 4-5 Å from the ligand. Probably a better approach would be to dock the ligand to pdb2. Could this be done through ChimeraX using Boltz2? Thank you for your suggestions.
George
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