Dear Dr. Murshudov, Thank in advance. I will try the version 5.6 to fix this problem.
Best wishes. On Tue, Jun 23, 2009 at 6:05 AM, Garib Murshudov <[email protected]>wrote: > 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 >> >> >> > -- 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]
