Re: [ccp4bb] refmac5.3 vs refmac5.4

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

Previous message:
Subject: Re: refmac5.3 vs refmac5.4
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-12-05

Next message:
Subject: Re: refmac5.3 vs refmac5.4
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-12-05

Subject: Re: refmac5.3 vs refmac5.4
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2007-12-05

On Dec 5, 2007, at 14:05, Jianghai Zhu wrote:

> Hi all,
>
> I updated refmac5.3 to refmac5.4 and found out that the reported
> RMSDs are quite different from these two versions even the refining
> protocols are the same.
>
> refmac5.3
> rmsBOND rmsANGLE rmsCHIRAL
> 0.006 0.694 0.046
>
> refmac5.4
> rmsBOND rmsANGLE rmsCHIRAL
> 0.015 1.150 0.004
>
> The R and Rfree are very similar from these two versions of
> refmac5. Does refmac5.4 have different geometry weights from
> refmac5.3? Which one is more reasonable?

besides the obvious answer that Garib gave (I agree...5.4 is better),
it might be good to remind (without going to the long previous
discussions about the best
rmsBOND), that its the users responsibility to choose correct weights.

having said this, its good to say that half the people will think
0.015 is better, and half that 0.006 is better.

what I find strange is the discrepancy in CHIRAL volumes rms, which I
can attribute either to a bug fix, a print error,
or drastically changed internal weighting between bonds and chiral
volumes.

A.

>
> Thanks.
>
> Jianghai
>
>
> +++++++++++++++++++++++++++++++
> Jianghai Zhu, Ph.D
> CBR Institute for Biomedical Research
> Department of Pathology
> Harvard Medical School
> 200 Longwood Ave., Boston, MA 02115
> Ph: 617-278-3211
> Fx: 618-278-3232
> +++++++++++++++++++++++++++++++
>
>
>

CCP4bb navigation

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

Previous message:
Subject: Re: refmac5.3 vs refmac5.4
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-12-05

Next message:
Subject: Re: refmac5.3 vs refmac5.4
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-12-05