Editing User:Speleo3 (section)

=== load_mtz_cctbx: Load MTZ files with a [[CCTBX]] wrapper (3 files) ===

1) ~/bin/mtz2ccp4.sh

<source lang="bash">
#!/bin/bash
export PATH=/opt/ccp4/ccp4-6.5/bin:$PATH
exec cctbx.python ~/bin/mtz2ccp4.py "$@"
</source>

2) ~/bin/mtz2ccp4.py

<source lang="python">
#!/opt/ccp4/ccp4-6.5/bin/cctbx.python

import os
import sys
import tempfile

def mtz2ccp4maps(filename, prefix='map'):
    '''
Creates a temporary directory and dumps all maps from the given MTZ file
into this directory as CCP4 maps files. Returns the path of the temporary
directory.
    '''
    from iotbx.reflection_file_reader import any_reflection_file

    hkl_in = any_reflection_file(file_name=filename)

    temp_dir = tempfile.mkdtemp()

    for i_map, array in enumerate(hkl_in.as_miller_arrays()):
        if array.is_complex_array():
            fft_map = array.fft_map(resolution_factor=0.25).apply_sigma_scaling()
            map_filename = os.path.join(temp_dir,
                    prefix + '_' + '_'.join(array.info().labels) + '.ccp4')
            fft_map.as_ccp4_map(file_name=map_filename)

    return temp_dir

# print the name of the temporary directory to standard output
print mtz2ccp4maps(*sys.argv[1:])
</source>

3) ~/.pymolrc.py

<source lang="python">
@cmd.extend
def load_mtz_cctbx(filename, prefix=''):
    '''
DESCRIPTION

    Load all maps from an MTZ file, using the mtz2ccp4.sh wrapper which
    uses iotbx (cctbx).
    '''
    import subprocess
    import glob
    import shutil

    if not prefix:
        prefix = os.path.basename(filename).rpartition('.')[0]

    outdir = subprocess.Popen([os.path.expanduser('~/bin/mtz2ccp4.sh'),
        filename, prefix], stdout=subprocess.PIPE).stdout.readlines()[0].strip()

    for mapfilename in glob.glob(os.path.join(outdir, '*.ccp4')):
        cmd.load(mapfilename)

    shutil.rmtree(outdir)
</source>