[phenixbb] adp weighting in phenix.refine

Pavel Afonine pafonine at lbl.gov
Fri Apr 1 12:37:48 PDT 2011

Hi Hailiang,

I mentioned this paper to you yesterday:

"On atomic displacement parameters ..." ( 
http://www.phenix-online.org/newsletter/CCN_2010_07.pdf )

Sounds like you didn't have chance to have a look at it yet -:)

Both of your questions, this one below and yesterday's, are answered in 
the above article!

Actually, what's not explicitly written in that article is the formula 
you quoted (my mistake!, although it is in phenix.refine docs):

Etotal = wxu_scale * wxu * Exray + wu * Eadp

which is the refinement target for ADP optimization (similarly to 
refinement of coordinates).

All the best!

On 4/1/11 12:18 PM, zhangh1 at umbc.edu wrote:
> Hi,
> In the manual of phenix.refine, it mentioned the weighting of adp term wrt
> Exray:
> *******************
> Etotal = wxu_scale * wxu * Exray + wu * Eadp
> *******************
> I understand what is the geometry weighting, but for adp, could somebody
> explain more about what is Eadp (or references)?
> By the way, for curiosity, I want check into the source code for details.
> To save some time, can somebody direct where the source code part is
> located for this Eadp calculation?
> Thanks!
> Best Regards, Hailiang
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