[ccp4bb] Tweaking with SCBUlk and BBULk parameters in refmac

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CCP4bb <-- 2007 <-- August 2007 <-- 03 August 2007

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From: Anthony Addlagatta anthony {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2007-08-03

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Date: 2007-08-03

Subject: Tweaking with SCBUlk and BBULk parameters in refmac
From: Jose Antonio Cuesta-Seijo jcuesta {- at -} UHNRES {- dot -} UTORONTO {- dot -} CA
Date: 2007-08-03

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: jcuesta@uhnres.utoronto.ca
**************************************

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CCP4bb <-- 2007 <-- August 2007 <-- 03 August 2007

Previous message:
Subject: Re: Volume calculation of a crevice
From: Anthony Addlagatta anthony {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2007-08-03

Next message:
Subject: Job: RNA Center in Santa Cruz, CA, US
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-08-03