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 -- modeller-care@salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage