I need to generate multiple pdb files for a single protein, each pdb file with different mutations, up to every single permutation possible for a selected region of a protein. For example, if I want to mutate every single residue in a region in the protein which is 3 residues long, I would have 3!=6 different permutations, and generate 6 different pdb files, each with a different sequence in the mutated region. I could do this manually in Meastro, or Pymol, or VMD, but that wouldn't be very time-efficient; is there anyway to make a script which could do this?
Here I leave a script to do what you ask in the statement. to execute it, open pymol and type "run /location_of_script/mutation.py". in the script you can define several proteins, residues that you want to mutate and the amino acid.
Remember that mutagenesis can bring clashes and it is a good practice to manually select the rotamers of the mutated residues
If I wanted to mutate residues on a specific chain of the protein, am I capable to specify which residues of a specific chain?
In the line:
prot_list = [['1shr', 'B']] # example [['1nzp', 'A'], ['4oxn', 'B']]
you have a list of object IDs and chain IDs, e.g. ['1shr', 'B'] denotes chain B in object 1shr.
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