Hi Anasuya,
your "pdbid" variable actually holds the file name (including
extension), so the delete statement fails.
Fix it like this:
cmd.delete(pdbid.split('.')[0])
Cheers,
Thomas
Anasuya Dighe wrote, On 03/02/12 19:38:
> 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.
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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