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
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 ?
Christopher Mohr wrote: > is there the possibility to create a representation of the superposition > of two proteins in MODELLER?
Of course - it would be a bit useless to make a superposition if you couldn't visualize it in some fashion. ;)
> 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 ?
I don't quite understand your question. superpose fits the second model onto the first, translating and/or rotating the second model accordingly. So once that is done you can write out the second model with model.write() as a PDB file (the coordinates of the first model are not changed, so there is no need to write it out). Then just load the first model and that rotated/translated version of the second model in your favorite PDB viewer to see the superposition. The output *.fit file is just a regular PDB file - no modification is necessary.
Ben Webb, Modeller Caretaker