BiologicalUnit/Quat

Note: PyMOL 1.8 can load biological units from mmCIF files with the assembly setting.

Included in psico This command or function is available from psico, which is a PyMOL extension.
Module	(biomolecule) psico.xtal (biomolecule)

This script does more or less the same as BiologicalUnit. It creates the quaternary 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 and (if available) in your local PDB mirror.

Also available from psico, but the command is called biomolecule instead of quat.

Example Usage

fetch 3bw1, type=pdb
quat 3bw1
as cartoon

The Code

'''
(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, type=pdb
    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)

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See Also

• BiologicalUnit
• Supercell
• assembly