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



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
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             https://salilab.org/modeller/
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