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

[Ecem Güngör]

Thanks a lot. But even I compare the atomic positions of the model and the
original structures, it still shows a difference. By the way, this
difference is not big but not understanding the protocol through Chimera
documentation made me a bit annoyed. But it is still okay.

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.
If this is the case, it might be good to explain what the standard
protocol means somewhere in the Chimera documentation. Otherwise, it might
be a bit confusing.

I will keep my eyes on the updates. Thanks a lot!


Eric Pettersen <pett at cgl.ucsf.edu>, 12 Ara 2022 Pzt, 20:27 tarihinde şunu
yazdı:

> This *seems* like a bug in both Chimera and ChimeraX.  I will open a
> ticket in our bug-tracking database with you cc'ed so that you will be
> notified when it gets fixed.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Dec 12, 2022, at 11:15 AM, Elaine Meng via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
>
> Hi Ece,
> As far as I know they should not move.
>
> If you are showing ribbons (not just atomic coordinates) it might seem
> like there are changes because the ribbon is interpolated over multiple
> positions, so the ribbon might be in a slightly different place even at
> residues where the atoms have not moved, just because the ribbon path
> calculation now has more atoms to use.
>
> Otherwise I would not expect anything to move.  Hide ribbons, show all
> atoms... if you still see atoms in different positions then you could use
> Help... Report a Bug and attach data like the session, if you are willing
> to share the data.
> Elaine
>
> On Dec 12, 2022, at 11:08 AM, Ecem Güngör via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
>
> Dear Elanie,
>
> Thanks for your answer.
>
> Even if I set the option you mentioned to 0, it still moves some positions
> of the atoms. That's why I could not comprehend the reason.
>
> Ece
>
>
> Elaine Meng <meng at cgl.ucsf.edu>, 12 Ara 2022 Pzt, 17:39 tarihinde şunu
> yazdı:
> Hi Ece,
> There is an option "Allow this many residues adjacent to missing regions
> to move" which you can change to zero instead of the default of one.  Then
> it should not change any atom positions.
>
> See the documentation:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#building
> >
>
> I don't know the details of the "standard" option, maybe others can
> elaborate. As mentioned in the documentation, if you choose the DOPE option
> instead, it may produce higher-quality results, but it takes longer and is
> also more prone to calculation failure.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Dec 12, 2022, at 5:38 AM, Ecem Güngör via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
>
> Hello,
>
> I have a protein crystal structure where some regions are not resolved in
> the crystal. Therefore, I want to predict and fill these regions, without
> touching the rest, by using the Model Loops/Refine Structure option of
> Modeller in Chimera. When I select the non-terminal missing structure as a
> model and standard as a loop modeling protocol, some atoms in the rest of
> the structure are shifted from the original positions. However, I want to
> keep them as they are. Here I would like to ask what standard loop modeling
> protocol corresponds to. Does it also refine or optimize the structure as a
> whole? What does it actually correspond to?
>
> Any help would be appreciated. Thanks.
>
> Ece
>
>
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