Well - this (expert??) would suggest using SCALE SIMPLE -
SCBULK is a fudge which has some theoretical justification if you have
measured very complete and accurate low resolution data, but seeing most
people havent done this it remains a fudge factor
The justification is related to average scattering from the solvent
which falls off rapidly with resolution - the BFIX is an attempt to
describe this. Obviously some solvent continuums behave differently to
others ..
Have you looked at your <F> distributions? There is a loggraph of them
in the REFMAC logs, and at data processing too.
Eleanor
Jose Antonio Cuesta-Seijo wrote:
Dear All,
I have a structure to 1.65A crystallized in high sulphate conditions.
The R factors went smoothly to 21% and 23% (Rfree), but the difference
map shows positive difference peaks in otherwise normal regions of the
main chain and is more noisy than expected in general. Since the
electron density in the solvent is much higher than that of water
(approx. 2M sulphate) I suspected of the solvent scaling. Tweaking
with SCBUlk and BBULk produced indeed a 0.5% improvement in R and a
0.3% improvement in Rfree. I have been doing this from the ccp4i
interface by changing the command line through the run and view com
file to
scal -
type BULK -
reso 1.648 20.0 -
LSSC FIXB SCBU 0.0 BFIX 200.0 - (those are the numbers tweaked with)
ANISO
I am running refmac version 5.2.2005
The SCBUlk parameter has a minimum for both R and Rfree at 0.0.
Variations of BBULk from 200.0 at that SCBUlk of 0.0 had no effect on
the R factors up to the 6th digit and I believe the refinement is
exactly the same. Changing BBULk at SCBUlk values different from 0.0
does have an effect on R and Rfree. Also, the R factors behave
symmetrically relative to SCBUlk, that is, SCBUlk 0.2 produces the
same results as SCBULK -0.2
What is the excat meaning/use of those parameters?
How are the experts going around with optimizing these?
Thanks,
Jose Antonio Cuesta Seijo.
**************************************
Jose Antonio Cuesta-Seijo
Cancer Genomics and Proteomics
Ontario Cancer Institute, UHN
MaRS TMDT Room 4-902M
101 College Street
M5G 1L7 Toronto, On, Canada
Phone: (416)581-7544
Fax: (416)581-7562
email: [EMAIL PROTECTED]
**************************************
