Re: [ccp4bb] Tweaking with SCBUlk and BBULk parameters in refmac

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Systems Biology Session: Diamond User Meeting 2007
From: "Brandao-Neto, J (Jose)" jose {- dot -} brandao-neto {- at -} DIAMOND {- dot -} AC {- dot -} UK
Date: 2007-08-06

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From: Klemens Wild Klemens {- dot -} Wild {- at -} BZH {- dot -} UNI-HEIDELBERG {- dot -} DE
Date: 2007-08-06

Subject: Re: Tweaking with SCBUlk and BBULk parameters in refmac
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-08-06

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

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Next message:
Subject: Hg rippled summary
From: Klemens Wild Klemens {- dot -} Wild {- at -} BZH {- dot -} UNI-HEIDELBERG {- dot -} DE
Date: 2007-08-06