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