[phenixbb] Refinement with optimize weights

Pavel Afonine pafonine at lbl.gov
Fri Sep 16 09:46:38 PDT 2011


have a look at "Improved target weight optimization in phenix.refine" 
article here:

and, make sure you are using the latest version of PHENIX - this is 

>  I wanted to know what parameters should I use for subsequent refinement.

Which parameters do you mean? Optimal weights are determined per 
refinement run. It is not given that in a next refinement run the 
optimal weights will be the same as in previous one.
Since weights optimization takes a long time to run (if you have 
multiple cpu machine then it can be run in parallel), normally you run 
it towards the end of refinement and not all the way through.

>  I would like to know what Fix X-ray/stereochemistry weight and Fix 
> X-ray/ADP weights are for?

In case you have your own weight values, you can specify them and then 
phenix.refine will use them as is.


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