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
