To keep the original residue numbers from the gro file, you could also
temporarily store additional numbering in the segment identifier, and
after loading get it back from there:
_pdbline = "ATOM %5i %-3s %3s%2s%4i" +\
" %8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s \n"
def pdbOut(atom,i=1):
segi = '%02d%02d' % (i/100000,atom[2]/10000)
stuff = [i%1e5,atom[0][:3],atom[1],atom[3],atom[2]%1e4] +\
list(atom[4:])+[1,40,segi,atom[0][0]]
return _pdbline % tuple(stuff)
And after cmd.read_pdbstr:
cmd.alter(objname, '(ID,resi,segi)=' +\
'(ID+100000*int(segi[:2]), resv+10000*int(segi[2:]), "")')
Cheers,
Thomas
On 08/18/2011 10:40 AM, Tsjerk Wassenaar wrote:
> Hi Joseph,
>
> Sorry about that. A bit naive with the numbering. To fix it, change the
> function
>
> def pdbOut(atom,i=1):
> return _pdbline%((i,) + (atom[0][:3],) + (atom[1],) + (atom[3],) +
> (atom[2],) + atom[4:] + (1,40) + (atom[0][0],))
>
> to
>
> def pdbOut(atom,i=1):
> stuff =
> [i%1e5,atom[0][:3],atom[1],atom[3],atom[2]%1e4]+list(atom[4:])+[1,40,atom[0][0]]
> return _pdbline % tuple(stuff)
>
> It worked for me on a .gro file with 160k atoms :)
>
> Cheers,
>
> Tsjerk
>
> 2011/8/18 Joseph André<andrejos...@gmail.com>:
>> Hi Tsjerk,
>> Thanks for the script. It works great on my protein. However when I try to
>> load the solvated system> 100.000 atoms I have problems with water
>> molecules. Is it possible to handle gro files with more than 100.000 atoms
>> and 9999 residues?
>> Best
--
Thomas Holder
MPI for Developmental Biology
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