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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: > To: > CC: > 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 > -- > http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > _______________________________________________ > modeller_usage mailing list > > https://salilab.org/mailman/listinfo/modeller_usage |