BiologicalUnit/Quat - Revision history

Cchem: 1 revision

2016-09-19T02:19:30Z

1 revision

Speleo3: assembly

2016-09-01T13:41:29Z

assembly

Bell: 2 revisions

2016-02-08T05:26:39Z

2 revisions

Pavel: /* The Code */

2016-02-04T18:27:19Z

The Code

Pavel: /* Example Usage */

2016-02-04T18:26:53Z

Example Usage

Pyadmin: 1 revision

2014-03-28T01:31:15Z

1 revision

Speleo3: created

2011-03-12T11:08:37Z

created

New page

This script does more or less the same as [[BiologicalUnit]]. It creates the '''quat'''ernary structure (BIOMOLECULE 1 assembly) from the REMARK 350 header.

This script is convenient to use because it searches automatically for the PDB file in the current directory, in [[Fetch_Path|fetch_path]] and (if available) in your local PDB mirror.

= Example Usage =
<source lang="python">
fetch 3bw1
quat 3bw1
as cartoon
</source>

= The Code =
<source lang="python">
'''
(c) 2010-2011 Thomas Holder, MPI for Developmental Biology

Module for reading REMARK records from PDB files and in particular
generate quaterny structure from REMARK 350.
'''

import sys, os
from pymol import cmd, stored

local_mirror_divided = '/mnt/bio/db/pdb.divided'

def pdbremarks(filename):
'''
Read REMARK lines from PDB file. Return dictionary with remarkNum as key
and list of lines as value.
'''
remarks = dict()
if not isinstance(filename, basestring):
f = filename
elif filename[-3:] == '.gz':
import gzip
f = gzip.open(filename)
else:
f = open(filename)
for line in f:
recname = line[0:6]
if recname == 'REMARK':
num = int(line[7:10])
lstring = line[11:]
remarks.setdefault(num, []).append(lstring)
return remarks

def quat350(rem350):
'''
Get transformation matrices for biomolecule 1 from REMARK 350.
'''
biomt = dict()
chains = tuple()
seenbiomolecule = False
for line in rem350:
if line.startswith('BIOMOLECULE:'):
if seenbiomolecule:
break
seenbiomolecule = True
elif line.startswith('APPLY THE FOLLOWING TO CHAINS:'):
chains = tuple(chain.strip() for chain in line[30:].split(','))
elif line.startswith(' AND CHAINS:'):
chains += tuple(chain.strip() for chain in line[30:].split(','))
elif line.startswith(' BIOMT'):
row = int(line[7])
num = int(line[8:12])
vec = line[12:].split()
vec = map(float, vec)
biomt.setdefault(chains, dict()).setdefault(num, []).extend(vec)
return biomt

def quat(name=None, filename=None, prefix=None, quiet=0):
'''
DESCRIPTION

Read REMARK 350 from `filename` and create biological unit
(quaternary structure)

USAGE

quat [name [, filename [, prefix]]]

ARGUMENTS

name = string: name of object and basename of PDB file, if
filename is not given {default: first loaded object}

filename = string: file path {default: <name>.pdb}

prefix = string: prefix for new objects {default: <name>}

EXAMPLE

fetch 1rmv
quat 1rmv
'''
quiet = int(quiet)
if name is None:
name = cmd.get_object_list()[0]
if prefix is None:
prefix = name
if filename is None:
candidates = [
'%s.pdb' % (name),
'%s/%s.pdb' % (cmd.get('fetch_path'), name),
'%s/%s/pdb%s.ent.gz' % (local_mirror_divided, name[1:3], name),
]
for filename in candidates:
if os.path.exists(filename):
break
else:
print 'please provide filename'
return
if not quiet:
print 'loading from %s' % (filename)
remarks = pdbremarks(filename)
if 350 not in remarks:
print 'There is no REMARK 350 in', filename
return
quat = quat350(remarks[350])
for chains in quat:
matrices = quat[chains]
for num in matrices:
mat = matrices[num][0:12]
mat.extend([0,0,0,1])
copy = '%s_%d' % (prefix, num)
if not quiet:
print 'creating %s' % (copy)
cmd.create(copy, '/%s//%s' % (name, '+'.join(chains)))
cmd.alter(copy, 'segi="%d"' % (num))
cmd.transform_object(copy, mat)
cmd.disable(name)
cmd.group('%s_quat' % (prefix), '%s_*' % (prefix))

cmd.extend('quat', quat)

# vi:expandtab:smarttab
</source>

= See Also =
*[[BiologicalUnit]]
*[[Supercell]]

[[Category:Script_Library]]
[[Category:Math_Scripts]]
[[Category:Structural_Biology_Scripts]]

← Older revision	Revision as of 02:19, 19 September 2016
(No difference)

@@ Line 1: / Line 1: @@
 This script does more or less the same as [[BiologicalUnit]]. It creates the '''quat'''ernary structure (BIOMOLECULE 1 assembly) from the REMARK 350 header.
@@ Line 140: / Line 144: @@
 *[[BiologicalUnit]]
 *[[Supercell]]
 [[Category:Script_Library]]
 [[Category:Math_Scripts]]
 [[Category:Structural_Biology_Scripts]]

← Older revision	Revision as of 05:26, 8 February 2016
(No difference)

@@ Line 91: / Line 91: @@
 EXAMPLE
-     fetch 1rmv
+     fetch 1rmv, type=pdb
      quat 1rmv
      '''

@@ Line 5: / Line 5: @@
 = Example Usage =
 <source lang="python">
-fetch 3bw1
+fetch 3bw1, type=pdb
 quat 3bw1
 as cartoon

← Older revision	Revision as of 01:31, 28 March 2014
(No difference)