[phenixbb] ADP: fix_wxu and wxu_scale

Pavel Afonine pafonine at lbl.gov
Tue Jan 25 10:08:54 PST 2011

  Hi Fulvio,

to better understand this I recommend you to have a look at this article 
"On atomic displacement parameters (ADP) and their parametrization in 
PHENIX" here:


A quick reply:

the target function for ADP refinement is:

T = T_xray * wxu_scale * wxu + T_restraints * wu

Obviously, by making wxu_smaller you will put more emphasis on 
restraints. wxu is determined by the program, and wxu_scale is to allow 
the user to do adjustments (if needed or desired).

If you use fix_wxu then the target is

T = T_xray * fix_wxu + T_restraints

I would play with wxu_scale either manually or let phenix.refine to find 
a good value automatically (optimize_wxu=True, or whatever is the 
equivalent in the GUI). There is some information in the manual:

Let me know should you have any questions.


On 1/25/11 3:36 AM, fulvio saccoccia wrote:
> Dear Phenix users and developers,
> 	I'm trying to refine a 3 A resolution structure. In order to better
> understand how can I use wxu_scale and fix_wxu options in phenix.refine,
> may you explain me their use, since I have a lot of problems with ADPs?
> In fact, I have big variations between atoms of the same residue.
> So, is it better to use wxu_scale or to impose fix_wxu to refine the
> ADPs?
> Thanks to all
> Fulvio Saccoccia

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