[phenixbb] how to generate a set of alternative conformations ?
Pavel Afonine
pafonine at lbl.gov
Tue Mar 29 08:04:17 PDT 2016
Hi Cedric,
> 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:
http://phenix-online.org/phenix_data/afonine/fem/fig_24_25_26_rsr_3I9Q/fig_25_ensemble_1000x1000.png
Command:
phenix.dynamics model.pdb random_seed=3456879 temperature=600
number_of_steps=500 stop_at_diff=0.5
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.
Pavel
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