Lothar Esser wrote:
[snip]
> 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:
xrefin
update
optimize overall {*Optimize overall
B-factor.*}
drop=0.01 {*This avoids overshooting the
minimum.*}
nstep=15
end
end
Although your q=0 atoms are not included in structure factor calculation
used for determining what the global B-factor shift was, which was
-0.17,
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:
xrefin
update
optimize group {*Optimize group
B-factor.*}
b=(attr q>0.0) {* Group all atoms with occ >0 *}
drop=0.01 {*This avoids overshooting the
minimum.*}
nstep=15
end
end
That would only apply the shift to atoms with occupancies greater than
zero.
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
_______________________________________________________________________
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