Hi I think there you're confusing overall aniso scaling of the Fcalc's to the Fobs's (normally the default) which is controlled by SCALE LSSC ANISO, and refinement of individual atomic displacement parameters controlled by REFI BREF ISOT/ANISO. In the script aniso scaling is turned on (even though it's the default) and there were no Bij's output.
-- Ian > -----Original Message----- > From: Benini, Stefano [mailto:[EMAIL PROTECTED] > Sent: 20 September 2007 09:56 > To: Ian Tickle > Subject: RE: [ccp4bb] anisotropic scaling in refmac versions > > I think it has nothing to do with versions of refmac (which > has been always very reliable!) > > I thought it could be because in one of the scripts the guy > had the B factor refinement as ISOT > > > > > refi - > > > > type REST - > > > > resi MLKF - > > > > meth CGMAT - > > > > bref ISOT > > as you can see in the original posting > > and I guess that scaling aniso would not refine B factor > anisotropically > > best regards > > Stefano > > *********************************************** > Stefano Benini PhD > Structural Biology - DECS > Mereside 50S38 > Alderley Park > Phone:+44-1625-518293 (ext.: 28293) > http://structuralbiology-ap.rd.astrazeneca.net/people/Stefano- > Benini/Stefano-Benini.html > ************************************** > > > -----Original Message----- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] > Behalf Of Ian > Tickle > Sent: 20 September 2007 08:32 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] anisotropic scaling in refmac versions > > > I can't say because I didn't install 0037 (I went straight > from 5.2.0019 to 5.3.0040 so I was blissfully unaware of the > problem!). However according to the original posting it's > easy to tell because if the alleged bug is present you don't > see the overall Bij terms in the output PDB file. > > HTH > > -- Ian > > > -----Original Message----- > > From: [EMAIL PROTECTED] > > [mailto:[EMAIL PROTECTED] On Behalf Of Nalam, Madhavi > > Sent: 19 September 2007 14:57 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: RE: [ccp4bb] anisotropic scaling in refmac versions > > > > I used Refmac 5.3.0037 to refine a structure. Is there a > > problem with this version too? > > Thank you in advance, > > Madhavi > > > > > > -----Original Message----- > > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > > Behalf Of Ian Tickle > > Sent: Wednesday, September 19, 2007 8:21 AM > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] anisotropic scaling in refmac versions > > > > I think this isn't a problem in the latest version of Refmac > > (0040 I think), so try downloading it from the York site. > > > > -- Ian > > > > > -----Original Message----- > > > From: [EMAIL PROTECTED] > > > [mailto:[EMAIL PROTECTED] On Behalf Of Alejandro > > Buschiazzo > > > Sent: 19 September 2007 13:20 > > > To: Lari Lehtio > > > Cc: CCP4BB@JISCMAIL.AC.UK > > > Subject: Re: [ccp4bb] anisotropic scaling in refmac versions > > > > > > Hello, > > > I wonder if there was any direct answer to the question that > > > Lari made a > > > couple of days ago. > > > Sorry if I missed it, but I believe there wasn't any > > response to the > > > ccp4bb... > > > > > > thanks > > > > > > Alejandro > > > > > > > > > Lari Lehtio wrote: > > > > Dear All, > > > > > > > > I just came back from the beam line and started to continue > > > my work on a structure that I solved > > > > while collecting other data. I noticed that my R-factors > > > were a lot higher at home lab although > > > > I was using the exact same input files. > > > > > > > > I then noticed that the version was different: > > > > > > > > The one giving lower R-factors was > > > > Refmac_5.2.0019 version 5.2.0019 : 06/09/05 > > > > > > > > And the one giving higher: > > > > Refmac_5.3.0032 version 5.3.0032 : 02/16/06 > > > > > > > > I happened to have the older version also in my home pc, so > > > I tried again and indeed, 5.2.0019 > > > > gives lower R-factors. > > > > > > > > The input command is identical, but when I "diffed" the > > > pdb-files, I noticed that anisotropic > > > > scale is missing in the newer files. Did I make a mistake? > > > How can I turn it back on. > > > > > > > > Below is the diff output and the command used for refmac. > > > > > > > > Thank you in advance, > > > > > > > > ~L~ > > > > > > > > < REMARK 3 PROGRAM : REFMAC 5.2.0019 > > > > > > > >> REMARK 3 PROGRAM : REFMAC 5.3.0032 > > > >> > > > > < REMARK 3 R VALUE (WORKING + TEST SET) : 0.21101 > > > > < REMARK 3 R VALUE (WORKING SET) : 0.20867 > > > > < REMARK 3 FREE R VALUE : 0.25559 > > > > > > > >> REMARK 3 R VALUE (WORKING + TEST SET) : 0.23077 > > > >> REMARK 3 R VALUE (WORKING SET) : 0.22807 > > > >> REMARK 3 FREE R VALUE : 0.28228 > > > >> > > > > < REMARK 3 BIN R VALUE (WORKING SET) : 0.240 > > > > > > > >> REMARK 3 BIN R VALUE (WORKING SET) : 0.262 > > > >> > > > > < REMARK 3 BIN FREE R VALUE : 0.288 > > > > > > > >> REMARK 3 BIN FREE R VALUE : 0.343 > > > >> > > > > < REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.271 > > > > > > > >> REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.941 > > > >> > > > > < REMARK 3 B11 (A**2) : 2.35 > > > > < REMARK 3 B22 (A**2) : -1.99 > > > > < REMARK 3 B33 (A**2) : 0.32 > > > > > > > >> REMARK 3 B11 (A**2) : 0.00 > > > >> REMARK 3 B22 (A**2) : 0.00 > > > >> REMARK 3 B33 (A**2) : 0.00 > > > >> > > > > < REMARK 3 B13 (A**2) : 0.90 > > > > > > > >> REMARK 3 B13 (A**2) : 0.00 > > > >> > > > > > > > > > > > ______________________________________________________________ > > > _______________________ > > > > make check NONE > > > > make - > > > > hydrogen YES - > > > > hout NO - > > > > peptide NO - > > > > cispeptide YES - > > > > ssbridge YES - > > > > symmetry YES - > > > > sugar YES - > > > > connectivity NO - > > > > link NO > > > > refi - > > > > type REST - > > > > resi MLKF - > > > > meth CGMAT - > > > > bref ISOT > > > > ncyc 10 > > > > scal - > > > > type SIMP - > > > > reso 2.100 19.976 - > > > > LSSC - > > > > ANISO - > > > > EXPE > > > > solvent YES - > > > > VDWProb 1.4 - > > > > IONProb 0.8 - > > > > RSHRink 0.8 > > > > weight - > > > > MATRIX 0.1 > > > > monitor MEDIUM - > > > > torsion 10.0 - > > > > distance 10.0 - > > > > angle 10.0 - > > > > plane 10.0 - > > > > chiral 10.0 - > > > > bfactor 10.0 - > > > > bsphere 10.0 - > > > > rbond 10.0 - > > > > ncsr 10.0 > > > > labin FP=FP SIGFP=SIGFP - > > > > FREE=FreeRflag > > > > labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT > > > PHDELWT=PHDELWT FOM=FOM > > > > PNAME unknown > > > > DNAME unknown130907 > > > > RSIZE 80 > > > > END > > > > > > > > _______________________________________ > > > > > > > > Lari Lehtiö > > > > Structural Genomics Consortium > > > > Medical Biochemistry & Biophysics Dept. > > > > Karolinska Institute > > > > Stockholm, Sweden > > > > _______________________________________ > > > > > > > > > > > > > > > > > > > > > -- > > > Alejandro Buschiazzo, PhD > > > Research Scientist > > > Laboratory of Structural Biology > > > Pasteur Institute of Montevideo > > > Mataojo 2020 > > > Montevideo 11400 > > > URUGUAY > > > > > > Phone: +5982 5220910 int. 120 > > > Fax: +5982 5224185 > > > > > > > > > > > > Disclaimer > > This communication is confidential and may contain privileged > > information intended solely for the named addressee(s). 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