Dear Modellers,

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: examples/commands/superpose.py


# 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 ?

Thanks
Christopher