SCALE_NATIVE: Scaling native data
SCALE_NATIVE and SCALE_MIR are routines to read in MIR data from Scalepack output files or from other formatted files and to scale it and put it all in a file suitable for ANALYZE_MIR and SOLVE. They are ordinarily called as the first steps in a completely automated structure determination and are followed by ANALYZE_MIR and SOLVE. They can also be run on their own. The routines work best when the MIR data is reasonably complete. The routines assume that either:
(Note: the data can be amplitudes, not intensities if you read in the data with READFORMATTED and you specify the flag READ_AMPLITUDES)
For the second case, reflections with H K L corresponding to I+ and I- are treated as such. These choices are specified with the keywords "merged" or "unmerged". SCALE_NATIVE can read up to 4 data files and SCALE_MIR can read in up to 4 data files per derivative.
SCALE_NATIVE uses the first dataset you give it as a basis for setting the scaling of all the others. It reads in all the data, converts from I to F, maps it to the asymmetric unit, and uses the mapped data to localscale all the original unmapped datasets. The scaled datasets are then mapped to the asymmetric unit, merged, and written out to the file you specify with the keyword "scalednativefile" (default = "native_f.drg").
Sample script file for SCALE_NATIVE
!-----Command file to read in raw native data and scale it---- @solve.setup ! get our standard information read in logfile native.logfile ! write out most information to this file. rawnativefile native.int ! file with native data H K L Iobs Sigma usually unmerged ! data have not yet been reduced to the a.u. readdenzo ! data written by Scalepack read_intensities ! alternative is read_amplitudes scalednativefile native_f.drg ! output file with scaled native data scale_native ! scale this native dataset !-------------------------------------------------------------------------------
Keywords for SCALE_NATIVE:
RAWNATIVEFILE xxx.int File "xxx.int" will be read in as data for native
PREMERGED The data in all RAWMADFILEs have H K L and 4 columns:
I+, sigma, I-, sigma
UNMERGED The data in all RAWMADFILEs have H K L and 2 columns:
I, sigma
READDENZO The datafiles are written by Scalepack. For unmerged data
they will be read with the formatting:(6i4,i6,2i2,i3,2f8.0) and
nsym*2+1 lines are skipped at the top of the file. For
merged data the formatting is: (3i4,4f8.0) and
3 lines are skipped at the top of the file.
READFORMATTED The datafiles were not written by Scalepack.
They will be read with "*" formatting.
READ_INTENSITIES The data are intensities (default)
READ_AMPLITUDES The data are amplitudes
(This is valid only with READFORMATTED)
NSKIP n Skip exactly n lines at the top of each data file
NSKIP 0 Do not skip any lines at the top of each data file
NSKIP -1 Skip 0 lines at the top of each data file
unless the keywords READDENZO and PREMERGED
are set, in which case,skip NS*4+1 lines
where NS is the number of symmetry elements
in the space group (this is the # of lines in
a Scalepack header) [Default: NSKIP = -1]
RATMIN xx Minumum ratio of F/sig to read in data for a
reflection at all is xx [default=0.0]. This is
useful for eliminating weak data.
OVERALLSCALE Do not do local scaling; just an overall
scale factor for F+, F- at each wavelength.
Use this if you already have scaled the data
and you don't want any more scaling done.
SCALEDNATIVEFILE aa.drg Scaled native data Fnat,sig will be written to and
read from "aa.drg" (default="native_f.drg")