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@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