[phenixbb] how to generate a set of alternative conformations ?
pafonine at lbl.gov
Tue Mar 29 08:04:17 PDT 2016
> Is there a way with phenix, in a badly defined electron density area,
> to generate a set of different alternative conformations for a small
> protein fragment ?
you can run many dynamics trials each one with different random seed and
this will generate many different models, for example like this:
phenix.dynamics model.pdb random_seed=3456879 temperature=600
Here: temperature and number_of_steps will control variability of
models, stop_at_diff will terminate the job if RMSD between starting
model and current one is greater then defined value.
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