Thanks for your reply. I have now incoprated your change into my new script. 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?


Knut J



> Date: Wed, 1 Dec 2010 10:38:17 -0800
> From: modeller-care@salilab.org
> To: knutjbj@hotmail.com
> CC: modeller_usage@salilab.org
> Subject: Re: [modeller_usage] mutant two ore more residues
>
> On 12/01/2010 05:05 AM, Knut J Bjuland wrote:
> > I have made some modification to the mutant script at the modeller wiki.
> > The change may be seen as patch to the original file. I I whised to
> > change residue 1M and 3P to 1T and E3 in 1B72 is this the way to go. Ca
> > s.mutant be used to select two residues?
>
> Sure, you can mutate as many residues as you want. You just need to
> think about whether the mutated residues interact with each other at
> all, since you may want to adjust the optimization. For example, your
> current script optimizes the first mutated residue, and then the second
> mutated residue. Instead, you *might* want to optimize both residues
> simultaneously. You could do that by replacing:
>
> optimize(s, sched)
> optimize(s1, sched)
>
> with
>
> optimize(s | s1, sched)
>
> (selections are sets, so "s | s1" returns a new selection that is the
> union of the two selections, i.e. it contains atoms that are in s or s1.)
>
> A similar consideration may apply to your energy() calls.
>
> Ben Webb, Modeller Caretaker
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