Append ligand coordinates from one PDB to another
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
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
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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participants (2)
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Elaine Meng -
George Tzotzos