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STILL : b factor refinement in xplor-3.851

Yoram Puius puius at aecom.yu.edu
Mon Dec 2 14:57:57 EST 1996

Lothar Esser wrote:
>                         Before:    After:
>    all hydrogen atoms   q=0 b=0    q=0 b=-0.17
>           non-H atoms   q=0 b=100  q=0 b=99.83
> And as I said before this is independent of whether I include these
> atoms in the structure factor calculation or not.
> Is this a bug or am I doing something wrong ?
>   Thanks,
>           Lothar
> ____________________________________________________________________________
> Dr. Lothar Esser 
> Howard Hughes Medical Institute
> 5323 Harry Hines Blvd.
> Dallas Texas 75235-9050
> e-mail : esser at chop.swmed.edu

I think the quick answer is
	- not a bug
	- you're not doing anything wrong
	- and your refinement is probably A-OK (with respect to this, anyway)

You may have noticed that the B-factors of all these unselected atoms
went down by the same amount, i.e. 0.17 A^2.  My guess is that this is
from the portion of the brefinement file which performs global B-factor
optimiziation, which is a uniform shift to ALL B-factors:

   optimize overall                            {*Optimize overall
      drop=0.01                     {*This avoids overshooting the

Although your q=0 atoms are not included in structure factor calculation
used for determining what the global B-factor shift was, which was
the corrections was applied to them.

A simple fix is adding the line

vector do (b=100) (attr q=0.0)	! I think the syntax is right

which will set the B of all zero-occ atoms to 100.0.  I don't think
it's affecting your actual B-factor refinement at all.

Alternatively, I think you could switch the overall B-refinement to:

   optimize group                            {*Optimize group
      b=(attr q>0.0)		     {* Group all atoms with occ >0 *}
      drop=0.01                     {*This avoids overshooting the

That would only apply the shift to atoms with occupancies greater than
It shouldn't matter, anyway.

I hope my syntax is right!

	- Yoram

Yoram A. Puius                      Albert Einstein College of Medicine
mailto:puius at aecom.yu.edu           Department of Biochemistry
M.D.-Ph.D. student                  1300 Morris Park Avenue
5th year                            Bronx, NY  10461
No matter how many times I visit {New York City] I'm always struck by
the same thing: a yellow taxi cab.  - Scott Adams

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