Hi Sam,
you could do this with PyMOL in batch mode with a python script.
Something like this:
-------------------------------
out = open('out.txt', 'w')
def check_nc_distance(pdbfile):
from pymol import cmd
cmd.delete('*')
cmd.load(pdbfile)
for chain in cmd.get_chains():
sele_n = 'first (chain %s and name N)' % chain
sele_c = 'last (chain %s and name OXT)' % chain
try:
d = cmd.get_distance(sele_n, sele_c)
if 10 < d < 20:
print >> out, pdbfile, chain, d
except:
pass
import glob
for pdbfile in glob.glob('*.pdb'):
check_nc_distance(pdbfile)
-------------------------------
Cheers,
Thomas
Sam Jimmeson wrote, On 04/19/12 03:14:
> Hello,
> I'm trying to figure out a way to search the entire PDB and find
> proteins that have N-terminal(Calpha) to C-terminal(Calpha) through
> space distances of between 10-20A. I was trying to decide if CONTACT or
> DISTANG would be better to use for this, or if there is an easier way
> using some other tool. Has anyone else ever done this? Thanks for any
> advice.
> -Sam
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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