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Re: [modeller_usage] Superposition Problem

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
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage