[modeller_usage] How to make better conformational sampling of models using MODELLER?

[Mahesh VELUSAMY <>]

Hi All,
As per the suggestion given in the modeller that changing random seed 
would helps in producing different models. On this note I have tried to 
generate 100 models from single template and using different random 
seeds. It was mainly performed to know how changing random seed 
influencing on conformational sampling ?. Following the experiment I had 
observed that there was notable fluctuations on the sidechain 
orientations. But 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.
Following these observations I have a couple of questions for the 
modeller experts as follows:
When modeller says changing random seed helps in finding different 
models, does it meant for sidechain orientations or backbone?
Is it possible to produce models in modeller that will have more 
variations on the backbone and in terms of RMSD ?
Thanking you in advance