Re: [ccp4bb] Refmac refinement

- Protein crystallography

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

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Subject: Scientist position at Constellation pharmaceuticals
From: "Steve {- dot -} Bellon" steve {- dot -} bellon {- at -} CONSTELLATIONPHARMA {- dot -} COM
Date: 2010-01-04

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Subject: Re: Refmac refinement
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-01-04

Subject: Re: Refmac refinement
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2010-01-04

Hi Feng,

just my speculations (of course, the respective authors of the program
you use may provide you with a better answer):

In terms of refinement results, all pairs of numbers below look the same
to me (regardless the refinement program used):

0.192/0.250
0.191/0.247
0.202/0.254
0.194/0.255

that is, they are within "expected" deviations. Typically, a refinement
program does anisotropic scaling and bulk-solvent correction before
computing the R-factors. This step numerically is very sensitive to
almost everything, so it's not surprising at all that you observe these
small differences between different versions of the program.

Pavel.

On 1/4/10 9:35 AM, Feng Guo wrote:
> Hi,
>
> I have a question about the refinement by Refmac program in CCP4 package. I
> tried both the old version(1.4.4) and the latest version (2.0.5) for restrained
> refinement, and they gave me different result. For old version, it's
> 0.192/0.250--> 0.191/0.247, while for the latest version, R/Rfree=0.202/0.254-
> ->0.194/0.255. For both version, I use the weighting term of 0.05. I am
> wondering which version will be better? or I did something wrong? Thank you.
>
>
> Feng
>

CCP4bb navigation

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

Previous message:
Subject: Scientist position at Constellation pharmaceuticals
From: "Steve {- dot -} Bellon" steve {- dot -} bellon {- at -} CONSTELLATIONPHARMA {- dot -} COM
Date: 2010-01-04

Next message:
Subject: Re: Refmac refinement
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-01-04