Hi Lina,
as far as I know the secondary structure atom property is not state
specific, so you cannot assign per state. But you can split states to
individual objects. The DSSP plugin (I guess you are talking about
http://www.pymolwiki.org/index.php/DSSP) however does not deal well with
multiple objects (Hongbo, can you fix that?). The build-in command "dss"
does, maybe you can use that?
Example:
fetch 1d7q, async=0
as cartoon
split_states 1d7q
delete 1d7q
dss all
rebuild
http://pymolwiki.org/index.php/Split_States
http://pymolwiki.org/index.php/Dss
I can also offer you my own dssp script which works with multiple
objects, see attachment. It provides the PyMOL commands "dssp" and
"stride". Check "help dssp".
Cheers,
Thomas
lina wrote, On 09/16/11 17:45:
Hi,
a quick question,
how can update the ss for all states, not check one by one,
and run dssp and update ...
Thanks for any advice,
--
Best Regards,
lina
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
'''
(c) 2010 Thomas Holder, Max Planck Institute for Developmental Biology
PyMOL wrapper for DSSP and STRIDE
'''
from pymol import cmd, stored
from subprocess import Popen, PIPE
import tempfile, os
def _common_ss_alter(selection, ss_dict, ss_map, raw=''):
'''
DESCRIPTION
Shared code of 'dssp' and 'stride' functions.
'''
if raw != 'ss':
cmd.alter(selection, 'ss = ss_map.get(ss_dict.get((model,chain,resi)), "")',
space={'ss_dict': ss_dict, 'ss_map': ss_map})
if raw != '':
cmd.alter(selection, raw + ' = ss_dict.get((model,chain,resi), "")',
space={'ss_dict': ss_dict})
cmd.rebuild(selection, 'cartoon')
def dssp(selection='(all)', exe='dsspcmbi', raw=''):
'''
DESCRIPTION
Secondary structure assignment with DSSP.
http://swift.cmbi.ru.nl/gv/dssp/
ARGUMENTS
selection = string: atom selection {default: all}
exe = string: name of dssp executable {default: dsspcmbi}
raw = string: atom property to load raw dssp class into {default: ''}
EXAMPLE
dssp all, /sw/bin/dsspcmbi, raw=text_type
color gray
color red, text_type H
color orange, text_type G
color yellow, text_type E
color wheat, text_type B
color forest, text_type T
color green, text_type S
set cartoon_discrete_colors, 1
SEE ALSO
dss, stride
'''
ss_map = {
'B': 'S', # residue in isolated beta-bridge
'E': 'S', # extended strand, participates in beta ladder
'T': 'L', # hydrogen bonded turn
'G': 'H', # 3-helix (3/10 helix)
'H': 'H', # alpha helix
'I': 'H', # 5 helix (pi helix)
'S': 'L', # bend
' ': 'L', # loop or irregular
}
tmpfilepdb = tempfile.mktemp('.pdb')
ss_dict = dict()
for model in cmd.get_object_list(selection):
cmd.save(tmpfilepdb, '%s and (%s)' % (model, selection))
process = Popen([exe, '-na', tmpfilepdb], stdout=PIPE)
for line in process.stdout:
if line.startswith(' # RESIDUE'):
break
for line in process.stdout:
resi = line[5:11].strip()
chain = line[11].strip()
ss = line[16]
ss_dict[model,chain,resi] = ss
os.remove(tmpfilepdb)
_common_ss_alter(selection, ss_dict, ss_map, raw)
cmd.extend('dssp', dssp)
def stride(selection='(all)', exe='stride', raw=''):
'''
DESCRIPTION
Secondary structure assignment with STRIDE.
http://webclu.bio.wzw.tum.de/stride/
SEE ALSO
dss, dssp
'''
ss_map = {
'C': 'L',
'B': 'S',
'b': 'S',
'E': 'S',
'T': 'L',
'G': 'H',
'H': 'H',
}
tmpfilepdb = tempfile.mktemp('.pdb')
ss_dict = dict()
for model in cmd.get_object_list(selection):
cmd.save(tmpfilepdb, '%s and (%s)' % (model, selection))
process = Popen([exe, tmpfilepdb], stdout=PIPE)
for line in process.stdout:
if not line.startswith('ASG'):
continue
chain = line[9].strip('-')
resi = line[11:16].strip()
ss = line[24]
ss_dict[model,chain,resi] = ss_map.get(ss)
os.remove(tmpfilepdb)
_common_ss_alter(selection, ss_dict, ss_map, raw)
cmd.extend('stride', stride)
# tab-completion
cmd.auto_arg[0].update({
'dssp' : [ cmd.selection_sc , 'selection' , ', ' ],
'stride' : [ cmd.selection_sc , 'selection' , ', ' ],
})
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