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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