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

[Ecem Güngör]

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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