On 4/7/19 6:36 AM, malkeet singh Bahia wrote: > To my surprise, in the final model, the constructed loop of about 20 > amino acid is very weird and is folding back into the protein > (sandwiched between secondary structure) resulting in numerous clashes.
20 residues is a very long loop - you will need to build a *lot* of models (>1000) to stand a chance of reasonably sampling the conformational space. Once you filter out the poorly-scoring models, you should be left only with non-weird loops.
In some cases, the starting model (.IL file in PDB format) may be generated such that the optimizer can't recover. In this case you may want to look into overriding the build_ini_loop() method: https://salilab.org/modeller/9.21/manual/node95.html
Ben Webb, Modeller Caretaker