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src/b/i/biskit-2.4/scripts/Mod/modelling_example.py   biskit(Download)
    pm = Pymoler( )
    for t in traj:
        pm.addPdb( t )
 
    pm.show()

src/b/i/biskit-2.4/Biskit/Dock/Complex.py   biskit(Download)
 
            self.pm = Pymoler()
            self.pm.addPdb( c.rec(), 'rec' )
            self.pm.addPdb( c.lig(), 'lig' )
 
            lig_sphere.xyz = mathUtils.projectOnSphere( lig_sphere.xyz )
 
            self.pm.addPdb( rec_sphere, 'rec_sphere' )
            self.pm.addPdb( lig_sphere, 'lig_sphere' )
 

src/b/i/biskit-2.4/Biskit/Dock/Intervor.py   biskit(Download)
        pm = Pymoler()
 
        pm.addPdb( model, 'com' )
        pm.addPdb( rec, 'rec' )
        pm.addPdb( lig, 'lig' )
 
        if xwater:
            pm.addPdb( xwater, 'x-water' )
            pm.colorAtoms( 'x-water', xwater[profile] )
 
        if water:
            pm.addPdb( water, 'water' )

src/b/i/biskit-2.4/Biskit/Mod/Benchmark.py   biskit(Download)
        if self.local:
            pm = Pymoler()
            pm.addPdb( pdb, "m" )
            pm.addPdb( reference, "r" )
            pm.colorAtoms( "m", tmp_model.profile("rms_outliers") )

src/b/i/biskit-2.4/Biskit/Dock/PatchGeneratorFromOrbit.py   biskit(Download)
 
    pm  = Pymoler()
    pm.addPdb( model, 'all' )
 
    ms = [ model.take( N.nonzero(mask) ) for mask in r ]

src/b/i/biskit-2.4/Biskit/Dock/PatchGenerator.py   biskit(Download)
 
    pm  = Pymoler()
    pm.addPdb( model, 'o' )
 
    ms = [ model.take( N.flatnonzero(mask) ) for mask in r ]

src/b/i/biskit-2.4/scripts/Mod/analyse.py   biskit(Download)
    if options.has_key('s'):
        p=Pymoler()
        p.addPdb( folders[0] + a.F_FINAL_PDB )
        p.add('color_b')
        p.add('select na, b<0')

src/b/i/biskit-2.4/scripts/Biskit/pdb2xplor.py   biskit(Download)
 
        pm = Pymoler( )
        mname = pm.addPdb( xplorer.outname + '.pdb' )
        pm.add('select xray-wat, segi 1XWW')
        pm.add('select added-wat, segi 1WWW')