[phenixbb] structural validation and deposit format

Pavel Afonine PAfonine at lbl.gov
Fri Dec 11 13:04:26 PST 2009

On 12/11/09 12:55 PM, rui wrote:
> SO in the output pdb file, there are another set of lines start with 
> ANISOU, what are those, should I keep those? 

These are ADPs - Atomic Displacement Parameters, or B-factors. They are 
as important as atomic coordinates (almost) stored in ATOM records -:)

> I turned on the optimze_wxc and optimize_wxu flags in the GUI, it does 
> give better R/Rfree. Do I need to turn on every time or just use the 
> optimized weights, where I can find those optimized weight? In log file? 

Optimization of weights is usually time consuming and the default 
weights are just good most of the time. So I usually recommend running 
weights optimization as the last step to tune up your model. Of course 
there might be exceptions.
Since optimal weight may be different from run to run, they are not 
stored in .def file for the next runs.


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