Hi,
I am running this code on some pdb files: 12gs.pdb, 182l.pdb, 183l.pdb
____ CODE ____
from pymol import cmd
def process_line(x):
pdbid,res,chain,num = x.split()
cmd.load(pdbid)
cmd.select("target","(resn %s and chain %s and resi %s)"%(res,chain,num))
cmd.select("zone2","(br. (target expand 9 and not (target expand 4.5)) and not
resn HOH and not HET)")
cmd.save("%s-%s-%s-%s-zone2"%(pdbid,res,chain,num),"zone2")
cmd.delete(pdbid)
def process_all(filename):
for line in open(filename):
process_line(line)
process_all("try.txt")
__ try.txt:
12gs.pdb 0HH A 210
182l.pdb BZF A 401
183l.pdb DEN A 400
____
~Problems: The -zone2 file generated looks wierd.
1) It shows multiple residues at a particular position, as in the atoms appear
overlapped.
please look into this and let me know. However in the .pdb file, the atoms at
that corresponding position are not showing any multiple occupancy or anything
of that sort, they appear to be overlapped in someway in the zone2 file. In
case, I use the same two <<select>> commands on the pymol terminal and then save
the -zone2 manually, then nothing seems different with the zone generated.
What might be causing this error to occur?
2) Also the residues occurring in the zone which span multiple chains are
interspersed in the -zone2 file. As in, time and again, a residue from the A
chain comes up, among a sequence of residues in the B chain.
Is there some problem with the script? please help me out on this.
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