Many more thanks for the response On 25-01-2018 20:59, Modeller Caretaker wrote:
On 1/25/18 10:14 AM, Mahesh VELUSAMY wrote:It was mainly performed to know how changing random seed influencing on conformational sampling ?Changing the random seed has no influence on sampling. It merely results in different initial randomized structures, before sampling.
Got it.
when I aligned all the models against top model (DOPE SCORE) there was no variations on the backbone conformation and also in terms of RMSD.Modeller restrains the backbone to match your template(s), so this is expected.
Got it.
May I know how to do these both weakening homology-derived restraints and adjusting the weights (also let me know what do you mean by weights? It would be helpful if you give any examples or sources to read)Is it possible to produce models in modeller that will have more variations on the backbone and in terms of RMSD ?Sure, by weakening any homology-derived restraints. Either adjust the weights,
My interest is single point mutated sequences sharing similar length of query coverage. ( I have also tried mutated_model method to do the same but even in that case I end up with poor sampling with no backbone changes.)or provide an alignment with lower sequence identity.
Ben Webb, Modeller Caretaker