[phenixbb] ADP: fix_wxu and wxu_scale
pafonine at lbl.gov
Tue Jan 25 10:08:54 PST 2011
to better understand this I recommend you to have a look at this article
"On atomic displacement parameters (ADP) and their parametrization in
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
> Thanks to all
> Fulvio Saccoccia
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