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