Hello,
I have an X-ray structure where I want to model some loop regions. However, while modeling these loops, I do not want to either optimize or refine them. How should I proceed for that?
Any help would be appreciated.
Hello are the loop regions missing residues? Thanks:) Joel
On Wed, Dec 7, 2022 at 5:40 PM Ecem Güngör via modeller_usage < modeller_usage@salilab.org> wrote:
> Hello, I have an X-ray structure where I want to model some loop regions. > However, while modeling these loops, I do not want to either optimize or > refine them. How should I proceed for that? Any help would be appreciated. > > ZjQcmQRYFpfptBannerStart > This Message Is From an Untrusted Sender > You have not previously corresponded with this sender. > > ZjQcmQRYFpfptBannerEnd > Hello, > > I have an X-ray structure where I want to model some loop regions. > However, while modeling these loops, I do not want to either optimize or > refine them. How should I proceed for that? > > Any help would be appreciated. > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/ >
On 12/7/22 2:39 PM, Ecem Güngör via modeller_usage wrote: > I have an X-ray structure where I want to model some loop regions. > However, while modeling these loops, I do not want to either optimize or > refine them. How should I proceed for that?
"model", "optimize" and "refine" are essentially synonyms - they all mean "move some atoms in an attempt to reduce the value of the scoring function" so what you're asking for doesn't really make sense, unless I am not understanding you correctly. Do you perhaps mean that you want to model the loops without affecting the rest of the protein? If so, that's what the loop modeling protocol does by default; see https://salilab.org/modeller/10.4/manual/node36.html
Ben Webb, Modeller Caretaker
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Ecem Güngör -
Joel Subach -
Modeller Caretaker