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. > >> 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, 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)
> or provide an alignment with lower sequence identity. 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.)
> > Ben Webb, Modeller Caretaker