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