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
