[phenixbb] how to generate a set of alternative conformations ?

[Pavel Afonine]

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