Re: [ccp4bb] Influence of symmetry related molecules on a protomer conformation in crystal structures

2011-07-21 Thread Thomas Holder 

this is of course possible with PyMOL, try this:

pdbid, chain = '1a00', 'A'
cmd.fetch(pdbid, async=0)
cmd.symexp('__neighbors', pdbid, pdbid + ' and chain ' + chain, 5.0)
print 'Number:', len(cmd.get_object_list('(__neighbors*)'))
cmd.delete('__neighbors*')
cmd.delete(pdbid)

Cheers,
  Thomas

On 07/14/2011 01:48 PM, sukanta mondal wrote:

I know, in PyMOL using 'symexp' possible to generate symmetry related
molecules for a given crystal structure. But I'm looking for some
program/software (for batch) by which I can find out the number
of symmetry related molecules (distance cutoff= 5A) interacting with
a given chain in a crystal structure.

Thanking you,
suku
NIBIO, Osaka



--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

[ccp4bb] Influence of symmetry related molecules on a protomer conformation in crystal structures

2011-07-14 Thread sukanta mondal 
I know, in PyMOL using 'symexp' possible to generate symmetry related
molecules for a given crystal structure. But I'm looking for some
program/software (for batch) by which I can find out the number
of symmetry related molecules (distance cutoff = 5A) interacting with
a given chain in a crystal structure.

Thanking you,
suku
NIBIO, Osaka

Re: [ccp4bb] Influence of symmetry related molecules on a protomer conformation in crystal structures

2011-07-14 Thread vandana kukshal 
hi ,
in CCP 4 package u can run CONTACT program use NCONT to find symmetry
contacts only. u can Fix contact distance  minimum and maximum also .




On Thu, Jul 14, 2011 at 5:18 PM, sukanta mondal sukanta.mon...@gmail.comwrote:

 I know, in PyMOL using 'symexp' possible to generate symmetry related
 molecules for a given crystal structure. But I'm looking for some
 program/software (for batch) by which I can find out the number
 of symmetry related molecules (distance cutoff = 5A) interacting with
 a given chain in a crystal structure.

 Thanking you,
 suku
 NIBIO, Osaka




-- 
Vandana Kukshal
Postdoc Fellow
structure biology group
international Center For Genetic Engineering and Biotechnolgy
India