[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:



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.


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