Re: [modeller_usage] Do a loop refinment in order to mimic loop in a template

[Modeller Caretaker <>]

On 4/22/21 7:24 AM, Miguel Lacerda wrote:
> Is it possible to do a loop refinment of a model by giving the residue 
> range plus the template (which will hold the desired spatial location)? 

If you already know the "desired spatial location" then what are you 
trying to refine?

> The orientation of the loop in my model its different to  my template’s. 

Modeller does not use the template orientation for loops (many loops 
correspond to insertions anyway). The starting conformation for a loop 
is random and is influenced only by the termini positions. See the loop 
modeling paper or https://salilab.org/modeller/10.1/manual/node499.html

If you want to manually set the starting conformation for the loop, 
override the build_ini_loop() method:
https://salilab.org/modeller/10.1/manual/node96.html

	Ben Webb, Modeller Caretaker
--
             https://salilab.org/modeller/
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