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Re: [ccp4bb]: model bias in refmac5?
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Garib Murshudov wrote:
>
> > Dear All,
> >
> > I would like to get some opinions from people using
> > refmac5 about how
> > serious the model bias the map coefficient (FWT,
> > PHWT) would be.
>
> Could you please send me the log file and if
> necessary the data with the models to test? If your
> sigmaA values are not reasanable (B for sigmaA is
> close to 0.0 or something like that) then you could
> expect model bias especially at this resolution and
> at this stage. You can play with different parameters.
> Let say use SCALE TYPE SIMPLe and check differences.
> I am preparing version which suffers less from this
> problem.
>
> Garib
>
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Following are part of the log file which I think is relevant:
-----------------------------------------------------------------------------
Overall : scale = 1.744, B = 0.000
Babinet"s bulk solvent: scale = 0.589, B = 200.000
Partial structure 1: scale = 0.433, B = -81.028
Overall anisotropic scale factors
B11 =-11.61 B22 =-10.58 B33 = 22.19 B12 = 0.00 B13 = 0.00 B23 =
0.00
Overall sigmaA parameters : sigmaA0 = 0.991, B_sigmaA = 132.058
Babinet"s scale for sigmaA : scale = -0.001, B = 150.000
SigmaA for partial structure 1: scale = 0.141, B = 0.001
-----------------------------------------------------------------------------
The B for partial structure sigmaA is close to zero, was this causing
the problem?
Jinsong
--
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"The DAO is not a real DAO when it can be talked about."
---(DAO DE JING)
Jinsong Liu, Ph.D.
Tularik Inc. Phone: 650 825-7054
Two Corporate Drive Fax: 650 825-7320
South San Francisco, CA 94080, USA Email: jsliu@tularik.com
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