Boaz, If you had used the U option in SHELXPRO to update from .res to .ins the free R should have been included in the deposition PDB file by the B option!
George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Mon, 8 Oct 2007, Boaz Shaanan wrote: > A related but somewhat easier problem to fix, I would think, is the report of > overall-R-free value in the B option in shelxpro. The R-free value is > reported in the .lst and other o/p files but is not transmitted to the output > pdb. Here is an example: > > REMARK 3 DATA USED IN REFINEMENT. > REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 > REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 > REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 > REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 > REMARK 3 CROSS-VALIDATION METHOD : FREE R > REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM > REMARK 3 > REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). > REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1749 > REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : > REMARK 3 FREE R VALUE (NO CUTOFF) : > REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : > REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : > REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 44691 > REMARK 3 > REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). > REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.1635 > REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : > REMARK 3 FREE R VALUE (F>4SIG(F)) : > REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : > REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : > REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 35043 > > Best wishes, > > Boaz > ----- Original Message ----- > From: "George M. Sheldrick" <[EMAIL PROTECTED]> > Date: Monday, October 8, 2007 11:16 > Subject: Re: [ccp4bb] Rfree statistics in SHELXL > To: CCP4BB@JISCMAIL.AC.UK > > > SHELX is much older than the free R so this was added as an > > afterthought, > > and unfortunately I did not think of calculating R-free for just > > the outer > > resolution shell. There isn't an easy way of doing this without > > some > > programmeing effort. I also think that it is NOT a good idea, in > > the outer > > resolution shell you may only about 100 reflections in your free > > R set, so > > the free R value will have a very large esd and so could be > > misleading. > > George > > > > Prof. George M. Sheldrick FRS > > Dept. Structural Chemistry, > > University of Goettingen, > > Tammannstr. 4, > > D37077 Goettingen, Germany > > Tel. +49-551-39-3021 or -3068 > > Fax. +49-551-39-2582 > > > > > > On Mon, 8 Oct 2007, Oliv Eidam wrote: > > > > > Dear all, > > > > > > I used SHELXL for anisotropic structure refinement of high- > > resolution data > > > (1.3 Angstroem) and a reviewer asked me to include refinement > > statistics for > > > the outer most resolution shell in the crystallographic table. > > While R-factors > > > for the outer most resolution shell belong to the standard > > output in REFMAC or > > > CNS, it seems to me that SHELXL calculates R-factors only for > > reflections of > > > the work set. I also noticed that test reflections are missing > > in the > > > structure factor file (.fcf file) generated by shelxpro, > > preventing me to use > > > the [S] or [L] options in shelxpro to calculate R(free) statistics. > > > Is it simply not possible to calculate the R(free) factor for > > the outer most > > > shell after SHELX refinement? Or is there a problem with my > > SHELX program? > > > > > > Many thanks for your answers and suggestions, > > > > > > Oliv > > > > > > > > > -- > > > Oliv Eidam > > > > > > Department of Biochemistry > > > University of Zurich > > > Winterthurerstrasse 190 > > > 8057 Zurich, Switzerland > > > > > > Phone: 0041-44-635-6563 > > > Email: [EMAIL PROTECTED] > > > Web: http://www.bioc.uzh.ch/gruetter > > > NCCR: http://www.structuralbiology.ethz.ch > > > > > > > > > > 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 >
