Dear CCP4 Bulletin Board Readers:
First, I thank Dr. Perrakis for his response (please forgive the
lateness of my "thank you!"). For keeping both intensities and
amplitudes when converting from MTZ to CNS format, using the "Output
User" option followed by proper editing of the file does work. I
could run a script from the command line containing something of this
form:
mtz2various HKLIN /path/refl.mtz HKLOUT /path/refl.cv
OUTPUT USER -
'(' INDE ',3i5,' FOBS=',F10.2,' SIG=',F10.2,' IO=',F10.2,'
S=',F10.2,' TEST=',i6)'
labin FP=F_p SIGFP=SIGF_p DUM1=IMEAN_p DUM2=SIGIMEAN_p IDUM1=FreeR_flag
end
Afterwards, one can use the vi editor to edit the file in order to
change "SIG" to "SIGMA", "IO" to "IOBS", and "S" to "SIGI" . (Due to
the fact that mtz2various couldn't run with too many characters in
the format specification, the full CNS column labels need to be
inserted this way). The editor can also be used to change the freeR
flags to match the defaults used in CNS (similar to the "XPLOR"
output option in mtz2various).
I have not yet had the chance to try cctbx.
Thanks again!
Gregg
*******************************************
Gregg Crichlow
Dept. of Pharmacology
Yale University
P.O. Box 208066
New Haven, CT 06520-8066
*******************************************
On Oct 27, 2006, at 4:06 AM, Anastassis Perrakis wrote:
On Oct 27, 2006, at 2:02, Gregg Crichlow wrote:
Dear CCP4 Bulletin Board Readers:
I have noticed that, when converting MTZ files to XPLOR (or
CNS) format using CCP4i, I do not have options for having
intensities in the output file. I found a way to output the
intensites by using the "Run&View Com File" option, and then
editing the command script appropriately. However, when this is
done it only gave me intensities (and sigma(I)) but not both
intensities and SF amplitudes. The MTZ2various documentation that
I have says "If only FP SIGFP or IP SIGIP are assigned on LABIN,
then h k l FP SIGFP or h k l IP SIGIP is output." However, if I
assign I and SIGI as well as FP and SIGFP, it seems to ignore the
FP and SIGFP assignments, and only give me intensities. Is there
a way to get it to output both intesities and amplitudes?
What can I say ... you are right.
You can always use the OUTPUT USER option with something like:
OUTPUT USER -
'('IND',3i4,' F=',F10.1,' S=',F8.1,' I=', F8.1,' SI=',F8.1)'
labin DUM1=F_nat306 DUM2=SIGF_nat306 DUM3=IMEAN_nat306
DUM4=SIGIMEAN_nat306
and edit in the header manually later.
I am pretty sure though that cctbx has something more elegant since
phenix can read all these formats transparently (never tried I's
but a bit of RTFineM can tell you if its supposed to work).
On a related note, I was curious, although this is not a
problem, as to why the intensities found in the MTZ file,
resulting from a run of Scalepack2MTZ, are scaled with respect to
the input values from the '.sca' file. I noticed that the
intensities are different in the two files, and differ by a factor
of approximately 4.547891321. (The calculator I was using is set
to nine decimal places).
Thank you all very much.
The scaling is done so as the F000 / I000 to fit the declared
number of atoms during scaling.
The scalepack scale is simply arbitrary i think.
A.
Gregg Crichlow
--
*******************************************
Gregg Crichlow
Dept. of Pharmacology
Yale University
P.O. Box 208066
New Haven, CT 06520-8066
*******************************************
