Re: [ccp4bb] [ccp4bb summary] Is there an easy way to down-weight figures of merit?

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

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Subject: Is there an easy way to down-weight figures of merit?
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-07-12

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From: Jacqueline Vitali j {- dot -} vitali {- at -} CSUOHIO {- dot -} EDU
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Subject: Re: [ccp4bb summary] Is there an easy way to down-weight figures of merit?
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-07-12

Thanks to everyone who replied.

Doing this with HL coefficients just prior to solvent-flattening was
the least painful. I arbitrarily divided by two (see below).

Most importantly, the maps improved significantly, showing clear
nucleotide density for missing (unmodeled) RNA fragments where before
there were only uninterpretable blips.

On Jul 11, 2008, at 11:47 PM, Randy J. Read wrote:

> Hi Bill,
>
> The easiest thing is to scale down the HL coefficients, e.g. by
> dividing them by two. (Dividing by two has the effect of taking the
> square root of every value in the phase probability curve then
> renormalizing, which reduces the sharpness of the probability
> distribution without changing the positions of the peaks. It's also
> equivalent to increasing the underlying variance of sources of error
> in the phasing.)
>
> You could do this in sftools. It's likely that in some programs
> there's an option to provide a scale factor for the HL coefficients.
>
> Regards,
>
> Randy

AND ...

On Jul 11, 2008, at 11:36 PM, Thomas Edwards wrote:

> this sounds exactly what "blur" hl coeffs does in CNS.
> From their web pages:
>
>
> hlcoeff_blur.inp
>
>
> "Blur" Hendrickson-Lattman coefficients for use in refinement with
> the MLHL target
>
> The phase probability distribution is "blurred"
> by application of a scale factor (S) and a B-factor (B):
> HLA_new = S * e^(-B*s*s) * HLA_old
> HLB_new = S * e^(-B*s*s) * HLB_old
> HLC_new = S * e^(-B*s*s) * HLC_old
> HLD_new = S * e^(-B*s*s) * HLD_old
> This is performed to compensate for overestimation of phase
> accuracy which most often occurs after density modification
> or when probability distributions are derived from an
> atomic model.
> Warning: this should only be used when there is a good
> reason to believe the phases are biased. MAD or
> MIR
> phase probability distributions should usually
> not be modified in this way.
>
>
> Good Luck!
> Cheers
> Ed
>

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

Previous message:
Subject: Is there an easy way to down-weight figures of merit?
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-07-12

Next message:
Subject: MSCAN or DSCAN
From: Jacqueline Vitali j {- dot -} vitali {- at -} CSUOHIO {- dot -} EDU
Date: 2008-07-12