is there the possibility to create a representation of the superposition of two proteins in MODELLER? I've used the following example script to create the superposition of the two proteins:
# Example for: selection.superpose() # This will use a given alignment to superpose Calpha atoms of # one structure (2ctx) on the other (1fas). from modeller import * env = environ() env.io.atom_files_directory = ['../atom_files'] mdl = model(env, file='1fas') mdl2 = model(env, file='2ctx') aln = alignment(env, file='toxin.ali', align_codes=('1fas', '2ctx')) atmsel = selection(mdl).only_atom_types('CA') r = atmsel.superpose(mdl2, aln) # We can now use the calculated RMS, DRMS, etc. from the returned 'r' object: rms = r.rms drms = r.drms print "%d equivalent positions" % r.num_equiv_pos mdl2.write(file='2ctx.fit')
Do I have to use the outputed *.fit file to create a representation (*.pdb file for example) or is there any other possibility to create a representation to actually see the superpositioned structures of the proteins ?