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Re: [ccp4bb] anisotropic scaling in refmac versions |
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CCP4bb navigationCCP4bb <-- 2007 <-- September 2007 <-- 19 September 2007Subject: Re: anisotropic scaling in refmac versions From: Alejandro Buschiazzo alebus {- at -} PASTEUR {- dot -} FR Date: 2007-09-19 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 CCP4bb navigationCCP4bb <-- 2007 <-- September 2007 <-- 19 September 2007 |
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