[phenixbb] The individual site refinement for Low resolution data (~3.8A)

Pavel Afonine pafonine at lbl.gov
Sat Mar 19 00:30:03 PDT 2011

  Hi Yu,

> I set 'wxc_scale = 0.1', and also included secondary structure 
> restraints, reference model. 

Using Ramachandran restraints may be a good idea to use at this 
resolution too.

> The 'individual site' still give me higher Rfree and bigger gap 
> between Rfree and Rwork of my dataset (~3.8A).

"Higher" and "bigger" than what? Your statement above does not contain 
any information for me to comment on.

> Is the 'wxc_scale = 0.1' not tight enough?

If the default setting does not work for you, then you have two options:

1) let phenix.refine find optimal values for you automatically, using


or if this doesn't work for you too, then

2) keep trying different values for wxc_scale and wxu_scale until you 
hit the one that produces the results you like.


More information about the phenixbb mailing list