Hello there,
I carried out Protein-Protein docking using the Cluspro server, the problem is that Cluspro provides resulting models as one combined PDB, so I am asking I there is a way I can isolate them while preserving the interactions so I can study the interaction using Maestro or PDBePISa?
I attached a picture showing how Pymol can recognize the two different chains, but ineffectively Maestro and PDBePISA can regonzie them the same way.
To create PDB file for each chain:
a) in PyMOL, select the chain and save the selection as PDB file.
b) in text editor, delete one of the chains.
In PyMol, you can use the split_chains script to put each chain into a separate object (https://pymolwiki.org/index.php/Split_chains).
You can also directly save each chain into a separate pdb file:
save obj1_A.pdb, obj1 and chain A
or
save obj1_A.pdb, /obj1//A
saves only chain A of obj1 into a pdb file, the same with
save obj1_B.pdb, /obj1//B
for chain B, and so on
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