Hi Tim,
On Thu, 2012-04-19 10:07 EDT, Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote:
> Hi Thomas,
>
> your script requires to download the entire PDB first into one
> directory, doesn't it? While technically feasible, this might take a
> while and a little bit of disk space.
I keep a mirror of the 80000+ pdb files and while they are stored in
multiple directories name according to the 2 middle characters of the PDB
code, there is one directory called "all" with links to all the files. Total
disk space used for only the '.pdb' format files is 15GB. It takes a while
to download initially, but then the update script that runs once a week
takes only a 2 to 3 minutes.
There is a separate problem with Thomas' script, though. Many structures
do not have an "OXT" atom at the C-terminus of their polypeptide chains.
It is probably safer to select the C-terminus with:
sele_c = 'last (chain %s and name O and polymer) % chain
Cheers,
Rob
> Tim
>
> On 04/19/12 09:52, Thomas Holder wrote:
> > 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
--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University,
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821
<robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
