This case would happen if the program first decides that the number of
twin operators are several. But them to be twin cell should be
deformed. This deformation makes some of the reflections to be
equivalent to higher resolution reflections than they are.
After calculating Rmerge and twin fraction the program removes small
or insignificant twin domains. Then usually there are less twin
operators. And resolutin to be extended reflections to be equivalent
is much less. But the program forgot to calculate new "highest"
resolution.
It has now been fixed and the version is:
www.ysbl.york.ac.uk/refmac/latest_refmac.html
Regards
Garib
On 22 Jun 2009, at 11:26, Boaz Shaanan wrote:
I observe the same oddity for linux refmac 5.5.0092
Boaz
----- Original Message -----
From: Jiamu Du <[email protected]>
Date: Monday, June 22, 2009 7:11
Subject: Re: [ccp4bb] problem of Refmac refinement on twinning data
To: [email protected]
> I am using Refmac on a windows xp system.
>
> On Mon, Jun 22, 2009 at 12:05 PM, Jiamu Du
> <[email protected]> wrote:
>
> > Dear all,
> > I am using Refmac version 5.5.0088. The data are twinning, so
> the key word
> > 'twin' was added into the scripts.
> > The refinement result is as pasted below:
> >
> > REMARK 3 REFINEMENT.
> > REMARK 3
> PROGRAM : REFMAC 5.5.0088
> > REMARK 3
> AUTHORS : MURSHUDOV,VAGIN,DODSON
> > REMARK 3
> > REMARK 3 REFINEMENT TARGET :
> MAXIMUM LIKELIHOOD
> > REMARK 3
> > REMARK 3 DATA USED IN REFINEMENT.
> > REMARK 3 RESOLUTION RANGE HIGH
> (ANGSTROMS) : 2.30
> > REMARK 3 RESOLUTION RANGE LOW
> (ANGSTROMS) : 20.00
> > REMARK 3 DATA
> CUTOFF (SIGMA(F)) : NONE
> > REMARK 3 COMPLETENESS FOR
> RANGE (%) : 86.58
> > REMARK 3 NUMBER OF
> REFLECTIONS : 32643
> > REMARK 3
> > REMARK 3 FIT TO DATA USED IN REFINEMENT.
> > REMARK 3 CROSS-VALIDATION
> METHOD :
> THROUGHOUT> REMARK 3 FREE R VALUE TEST
> SET SELECTION : RANDOM
> > REMARK 3 R
> VALUE (WORKING + TEST SET) : 0.22929
> > REMARK 3 R
> VALUE (WORKING SET) : 0.22749
> > REMARK 3 FREE R
> VALUE : 0.26464
> > REMARK 3 FREE R VALUE TEST SET
> SIZE (%) : 4.9
> > REMARK 3 FREE R VALUE TEST SET
> COUNT : 1689
> > REMARK 3
> > REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
> > REMARK 3 TOTAL NUMBER OF BINS
> USED : 20
> > REMARK 3 BIN RESOLUTION RANGE
> HIGH : 2.296
> > REMARK 3 BIN RESOLUTION RANGE
> LOW : 2.355
> > REMARK 3 REFLECTION IN
> BIN (WORKING SET)
> : 0
> > REMARK 3 BIN COMPLETENESS
> (WORKING+TEST) (%) : 0.00
> > REMARK 3 BIN R
> VALUE (WORKING SET) : 0.000
> > REMARK 3 BIN FREE R VALUE SET
> COUNT : 0
> > REMARK 3 BIN FREE R
> VALUE : 0.000
> > REMARK 3
> > REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED
> IN REFINEMENT.
> >
> > Why are the value of REFLECTION IN BIN, BIN COMPLETENESS, BIN
> FREE R VALUE
> > SET COUNT, BIN FREE R VALUE all zero?
> > Another question is that, my data is of 2.38 angstron
> resolutiom, but
> > refinement result lists a high resolution of 2.3 angstrom.
> > If I did not add the keyword 'twin', all the results are normal.
> >
> > Thanks and best wishes.
> >
> > --
> > Jiamu Du, Ph.D.
> > State Key Laboratory of Molecular Biology
> > Institute of Biochemistry and Cell Biology
> > Shanghai Institutes for Biological Sciences
> > Chinese Academy of Sciences
> > 320 Yue-Yang Road
> > Shanghai 200031
> > P. R. China
> > Tel: +86-21-5492-1117
> > E-mail: [email protected]
> >
>
>
>
> --
> Jiamu Du, Ph.D.
> State Key Laboratory of Molecular Biology
> Institute of Biochemistry and Cell Biology
> Shanghai Institutes for Biological Sciences
> Chinese Academy of Sciences
> 320 Yue-Yang Road
> Shanghai 200031
> P. R. China
> Tel: +86-21-5492-1117
> E-mail: [email protected]
>
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan
