X-PLOR 3.8 B factor refinement

Yoram Puius puius at aecom.yu.edu
Mon Jan 26 20:35:24 EST 1998


M Roberts wrote:

> In the restrained individual B refinement (brefinement.inp),
> the maximum B value appears to be set at 100.0.
> Is it possible or advisable to change this to a higher limit?
> A number of my B values are truncated at this value.

Greater than 100 A^2?  Your atoms are not there.  Many people do
notbelieve that atoms with B>60 or so are truly there.  I don't know how
to
refine B>100, but nobody will take such a number seriously.

> Is it possible to refine an overall B value in X-PLOR 3.8,
> or is Fobs/Fcalc scaling still the only option at this time?

The code to do it is in $XPLOR/tutorial/xtalrefine/brefinement.inp, to
wit:

xrefin
  update
  optimize overall                                 {*refine overall
B-factor*}
    nstep=15
    drop=0.01
  end
end

> I notice that the scattering factors for the hydrogen atoms are
> not automatically included in the scattering factor library.
> Is it possible to retrieve them from somewhere or type them in
> by hand?
>

Most protein crystallographers don't need them.  From the "atominfo"
program, which I
think I found at the X-PLOR web site, I got the following output,
presumably drawn from
the international tables:

# atominfo H
1 "H" "hydrogen" 1.008
Scattering Factor Label (IT92): "H"
  IT92-CAA a1 b1 a2 b2 a3 b3 a4 b4 c
    0.493002 10.5109 0.322912 26.1257 0.140191 3.14236 0.04081 57.7997
0.003038
Scattering Factor Label (WK95): "H"
  WK95-CAA a1 b1 a2 b2 a3 b3 a4 b4 a5 b5 c
    0.413048 15.5699 0.294953 32.3985 0.187491 5.7114 0.080701 61.8899
0.023736 1.33412 4.9e-05
Atom Radius 0.78 "H"

I believe the first line of scattering factor numbers are appropriate
for X-PLOR.

Enjoy,
        Y

--
_______________________________________________________________________
Yoram A. Puius                Albert Einstein College of Medicine
6th year M.D.-Ph.D.           Department of Biochemistry
mailto:puius at aecom.yu.edu     1300 Morris Park Avenue, Bronx, NY  10461
        http://www.geocities.com/Athens/Forum/7504
_______________________________________________________________________






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