[phenixbb] adp weighting in phenix.refine

zhangh1 at umbc.edu zhangh1 at umbc.edu
Fri Apr 1 13:25:29 PDT 2011


Hi Pavel:

Yes, the formula of Eadp (Tadp) is exactly in the paper you sent me (sorry
I should have read it more carefully:-( By the way, since sometimes I may
want to check into the python codes for details, are there any sources for
the program archtecture description to make life easier (say to locate the
Eadp formula in phenix code)? Thanks!

Best Regards, Hailiang


> 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!
> Pavel.
>
>
> 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
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
>




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