Subject: Re: [modeller_usage] mutant two ore more residues
From: Modeller Caretaker <>
Date: Fri, 03 Dec 2010 16:09:38 -0800
Cc:
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.