Re: [modeller_usage] missing loop

[Qinghua Liao <>]

Dear Ben,

Thanks a lot for your guide. I just figured it out to use loopmodel to 
optimize the loop.
I am going to build up a large number of conformations of the loop by 
setting a.loop.ending_model to a large value.

Just another question, will set "a.ending_model" more than 1 help a 
little bit, as the total number will be a.ending_model * 
a.loop.ending_model?


All the best,
Qinghua

On 5/15/20 1:04 AM, Modeller Caretaker wrote:
> On 5/14/20 1:53 PM, Qinghua Liao wrote:
> > In my protein, there is one missing loop, 15 residues.
> ...
> > However, the loops added are too extended, even have bad contacts 
> > with the other parts of the protein.
>
> You are not doing any loop refinement, and are only building a single 
> model. That is extremely unlikely to sample anything close to the 
> correct loop conformation. You will need to employ loopmodel to 
> optimize the loop as per 
> https://salilab.org/modeller/9.24/manual/node34.html.
>
> Even so, 15 residues is a very long loop, about at the limit of what 
> Modeller's loop refinement algorithm can handle. You will need to do 
> extensive sampling of conformational space (by building multiple 
> models by setting a.loop.ending_model to a large value, perhaps 500 or 
> more) and then filter for the best models.
>
>     Ben Webb, Modeller Caretaker