Hi Julian,
A one-liner to create chain selections looks like this:
for c in cmd.get_chains(): cmd.select("chain_" + c, "chain " + c)
PyMOL doesn't provide access to the PDB header fields. In principle PyMOL
provides a way to access everything inside mmCIF files, see:
https://pymolwiki.org/index.php/Cif_keepinmemory
However, instead of doing this, I recommend to use the PDBe web API which
provides the data in a friendly JSON data structure. I've attached a Python
script which creates molecule (or chain) selections for 5n61 as an example. I
recommend to load PDB structures from mmCIF or MMTF format, which not only have
chain identifiers, but also molecule identifiers ("segi" field in PyMOL).
Hope that helps.
Cheers,
Thomas
> On Jun 12, 2017, at 12:21 PM, Julian Reitz <julianr1...@gmail.com> wrote:
>
> Dear all,
>
> I have a pdb-file with multiple chains (5N61).
>
> Is there an easy way to create selections for all the chains that are defined
> in the pdb-header (A to U) without doing it manually for every chain (select
> A, chain A)?
> Is it also possible to use the MOLECULE information from the header to name
> the selections?
>
> Thank you in advance,
>
> Julian
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
import json
import urllib2
from pymol import cmd
@cmd.extend
def pdb_chain_selections(code):
'''
DESCRIPTION
Make selections for every molecule (if loaded from mmCIF/MMTF) or
every chain (if loaded from PDB), using PDBe REST API.
'''
data = json.load(urllib2.urlopen(
'http://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/' + code))
# check if we can select by segi (label_asym_id)
has_segi = not cmd.count_atoms('segi ""')
for mol in data.values()[0]:
# only include polymers
if not mol[u'molecule_type'].startswith('poly'):
continue
# entity description (truncated)
desc = mol[u'synonym'][:200]
if has_segi:
# select molecules by label_asym_id (PyMOL 1.7.4+)
for chain in mol[u'in_struct_asyms']:
cmd.select('segi_%s_%s' % (chain, desc), 'segi ' + chain)
else:
# select chains
for chain in mol[u'in_chains']:
cmd.select('chain_%s_%s' % (chain, desc), 'chain ' + chain)
code = '5n61'
cmd.fetch(code)
pdb_chain_selections(code)
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