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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.
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
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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