Re: [PyMOL] Selection of chains based on PDB header
Dear Julian
You can also try the PDB plugin which places each chain into a selection
automatically for you.
https://pymolwiki.org/index.php/PDB_plugin
Regards
John
PDBe
On 12/06/2017 17:10, Thomas Holder wrote:
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 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.
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Re: [PyMOL] Selection of chains based on PDB header
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 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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