On 12/01/2010 11:56 PM, Knut J Bjuland wrote: > Thanks for your reply. I have now incoprated your change into my new > script.
There is no guarantee that my suggested change gives better results than your original script. I suggest you try both and see.
> I have also made one change to the energy function. > > for i in [s,s1]: > i.energy() > i.randomize_xyz(deviation=4.0) > > > Will this new change that I made cause the modeller to take into > account the affect one reside have on to another if they are neighbors?
That won't actually change anything at all. You are still calculating the energy for each residue individually. If you wanted to calculate the energy of the pair of residues simultaneously, use something like (s|s1).energy() The same disclaimer from above applies.
randomize_xyz simply randomizes the coordinates, with no consideration of steric clash etc., so it will make no difference whether you randomize both residues simultaneously or one at a time.
Ben Webb, Modeller Caretaker