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Difference between revisions of "Pse export version"

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Find polar pairs with the [[find_pairs|cmd.find_pairs]] function and return them as a list of atom pairs. It finds (more or less) the same contacts like [[distance|cmd.distance(mode=2)]].
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The [[pse_export_version]] setting switches to a legacy format when saving PSEs, so far possible. The value is the floating point number representation of the targeted legacy PyMOL version, for example '''1.74''' to save a session for PyMOL 1.7.4.
  
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== Example ==
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''New in PyMOL 1.7.6''
  
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<source lang="python">
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Session file loading is always backwards compatible, so any newer version of PyMOL can load old session files.
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pairs = polarpairs('chain A', 'chain B')
 
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for p in pairs:
 
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    dist = cmd.get_distance('(%s`%s)' % p[0], '(%s`%s)' % p[1])
 
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    print p, 'Distance: %.2f' % (dist)
 
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</source>
 
  
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== The Script ==
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== Examples ==
  
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<source lang="python">
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<syntaxhighlight lang="python">
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'''
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# current version (default)
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(c) 2011 Thomas Holder, MPI for Developmental Biology
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set pse_export_version, 0
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'''
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save current.pse
  
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from pymol import cmd
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# compatible with PyMOL 1.7.4
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set pse_export_version, 1.74
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save 174compat.pse
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</syntaxhighlight>
  
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def polarpairs(sel1, sel2, cutoff=4.0, angle=63.0, name='', state=1, quiet=1):
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== Known Limitations ==
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    '''
 
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ARGUMENTS
 
  
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    sel1, sel2 = string: atom selections
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The following objects are not or only partly supported:
  
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    cutoff = float: distance cutoff
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* scenes before 1.7.6 (support added in 1.8.4)
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* volumes before 1.7.2
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* ramps
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* CGOs
  
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    angle = float: h-bond angle cutoff in degrees. If angle="default", take
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== See Also ==
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    "h_bond_max_angle" setting. If angle=0, do not detect h-bonding.
 
  
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    name = string: If given, also create a distance object for visual representation
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* [[save]]
  
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SEE ALSO
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[[Category:Settings]]
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    cmd.find_pairs, cmd.distance
 
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    '''
 
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    cutoff = float(cutoff)
 
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    quiet = int(quiet)
 
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    state = int(state)
 
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    if angle == 'default':
 
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        angle = cmd.get('h_bond_max_angle', cmd.get_object_list(sel1)[0])
 
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    angle = float(angle)
 
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    mode = 1 if angle > 0 else 0
 
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    x = cmd.find_pairs('(%s) and donors' % sel1, '(%s) and acceptors' % sel2,
 
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            state, state,
 
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            cutoff=cutoff, mode=mode, angle=angle) + \
 
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        cmd.find_pairs('(%s) and acceptors' % sel1, '(%s) and donors' % sel2,
 
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            state, state,
 
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            cutoff=cutoff, mode=mode, angle=angle)
 
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    x = sorted(set(x))
 
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    if not quiet:
 
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        print 'Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle)
 
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        print 'Found %d polar contacts' % (len(x))
 
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    if len(name) > 0:
 
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        for p in x:
 
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            cmd.distance(name, '(%s`%s)' % p[0], '(%s`%s)' % p[1])
 
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    return x
 
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cmd.extend('polarpairs', polarpairs)
 
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</source>
 
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[[Category:Plugins]]
 
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[[Category:Biochemical_Scripts]]
 

Latest revision as of 00:07, 17 October 2016

The pse_export_version setting switches to a legacy format when saving PSEs, so far possible. The value is the floating point number representation of the targeted legacy PyMOL version, for example 1.74 to save a session for PyMOL 1.7.4.

New in PyMOL 1.7.6

Session file loading is always backwards compatible, so any newer version of PyMOL can load old session files.

Examples

# current version (default)
set pse_export_version, 0
save current.pse

# compatible with PyMOL 1.7.4
set pse_export_version, 1.74
save 174compat.pse

Known Limitations

The following objects are not or only partly supported:

  • scenes before 1.7.6 (support added in 1.8.4)
  • volumes before 1.7.2
  • ramps
  • CGOs

See Also

Retrieved from "http://wiki.pymol.org/index.php?title=Pse_export_version&oldid=13664"