[Chimera-users] Question about Model Loops Option in Chimera

[Ecem Güngör]

Thanks Elanie and others!




Elaine Meng <meng at cgl.ucsf.edu>, 13 Ara 2022 Sal, 17:33 tarihinde şunu
yazdı:

> Hi Ece (and others),
> The bug in Chimera and ChimeraX, now fixed in both programs, was that when
> you choose "0" residues allowed to move, it was still allowing 1 residue on
> each side of the loop to move. To get the fix, download the current daily
> build:
> <https://www.rbvi.ucsf.edu/chimera/download.html#daily>
>
> In the fixed version, if you model loops and specify "0" residues adjacent
> to the loop allowed to move, then it will follow those instructions:  all
> the atoms except for the loops/segments you are modeling will stay exactly
> in the same place.
>
> The protocol options (standard, DOPE, ...) are just which kind of scoring
> Modeller uses to choose the loop conformation, with DOPE being
> fancier/slower than the standard.  I think that is already mentioned in the
> Chimera help. It doesn't say much because I couldn't find much at the
> Modeller website, but I will try to make it better.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
> > On Dec 12, 2022, at 9:29 PM, Ben Webb via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > On 12/12/22 9:03 PM, Ecem Güngör via Chimera-users wrote:
> >> What I found on the Modeller website is that potentially all of the
> atoms in the final model could move since either AutoLoop or LoopModel will
> try to build a comparative model using the input PDB as a template. You can
> check this site <https://salilab.org/modeller/wiki/Missing_residues>for
> more.
> >
> > You are misinterpreting that text. Comparative modeling (which is what
> is described at that URL) will optimize the entire model by default
> (although you can ask it not to). Loop modeling of a given input structure
> will only move the loop atoms:
> > https://salilab.org/modeller/10.4/manual/node36.html
> > Of course, if you do comparative modeling followed by loop refinement,
> all the atoms will move because of the comparative modeling step.
> >
> > (I had thought my answer when you asked about this a week ago on the
> Modeller mailing list addressed your question, but if anything wasn't
> clear, please let me know.)
> >
> >       Ben
> > --
> > ben at salilab.org                      https://salilab.org/~ben/
> > "It is a capital mistake to theorize before one has data."
> >       - Sir Arthur Conan Doyle
> > _______________________________________________
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> https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
> >
>
>
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