A dumb script to convert methionines in a PDB file to their tellurium and selenium replacement mutants.

heavy_mutants.py

#!/usr/bin/env bash

"""
Generates a selenomethionine (MSE) or telluromethionine (MTE) mutant.

usage: ./heavy_mutant <pdb>
"""

import sys

mutation = raw_input("Mutate all METs to what {'MSE', 'MTE'}? ")

if mutation == 'MSE':
    mutation_code = 'MSE'
    heavy_atom    = 'SE'
elif mutation == 'MTE':
    mutation_code = 'MTE'
    heavy_atom    = 'TE'
else:
    raise ValueError('Can only do selenium/tellurium mutations right now!')


input_fn = sys.argv[1]
f = open(input_fn, 'r')
lines = f.readlines()
f.close()

# search lines for MET residues
newlines = []
n_met = 0

for l in lines:
    if l[17:20] == 'MET':
        l = l.replace('MET', mutation_code)
        
        # re-label
        if l[13] == 'S':
            n_met += 1
            l = l.replace('SD', heavy_atom)
            l = l[:76] + heavy_atom + '\n'
            
    newlines.append(l)
            

output_fn = input_fn[:-4] + '-' + mutation_code + '.pdb'
f = open(output_fn, 'w')
f.writelines(newlines)
f.close()

print "Mutated %d METs" % n_met
print "Wrote: %s" % output_fn