SCALE_MIR: Scaling derivative data to a native dataset
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_MIR reads in and converts the data from I to F, scales all the F- data in the derivative datasets to the F+ data, then it scales each derivative (F-, F+) to the native. All the scaling is done using LOCALSCALE. The F- and F+ data for the derivatives are separately merged and use to create two data files. The first contains Fnat,sigma, and (Fbar,sig,Delanom,sig) for each derivative. It is specified by the keyword "mirfbarfile" and is usually called "mir_fbar.drg". The other contains Fnat,sigma, and (F+,sig,F-,sig) for each derivative. It is specified by the keyword "mirfpfmfile" and is usually called "mir_fpfm.drg". If you don't want to use anomalous differences later, you can specify the "noinano" keyword for that derivative in SOLVE. At the end of the output for SCALE_MIR will be a summary of the scaling R-factors for isomorphous and anomalous differences and of the completeness of the datasets.
Sample script file for SCALE_MIR
!-----Command file to read in raw derivative data and scale it to the native---- @solve.setup ! get our standard information read in logfile deriv.logfile ! write out most information to this file. scalednativefile native_f.drg ! you need a native to scale the derivatives... derivative 1 ! about to enter information on derivative #1 rawderivfile deriv1.int ! the derivative data is in deriv1.int derivative 2 ! next derivative rawderivfile deriv2.int unmerged ! data have not yet been reduced to the a.u. readdenzo ! data written by Scalepack read_intensities ! data are intensities (alternative is read_amplitudes) scale_mir ! scale the derivs to the native !------------------------------------------------------------------------------
Keywords for SCALE_MIR:
RAWNATIVEFILE xxx.int File "xxx.int" will be read in as data for native
DERIVATIVE n The next RAWMIRFILE(s) that are read in will be
for derivative n
RAWDERIVFILE xxx.int File "xxx.int" will be read in as data for
the current derivative
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.
FPFM_ONLY Toss all acentric reflections where either F+
or F- is missing.
FP_OR_FM Use F+ or F- as an estimate of Fbar if F+ and
F- are not both present. This is useful if
your data is not that complete. It is
better to obtain complete data however.
This is the default for MIR 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
read from "aa.drg" (default="native_f.drg")
MIRFBARFILE xx.scl Output file with Fnat,sig, and (Fbar,sigma,DelAno,sigma)
for each derivative will be xx.scl
(DEFAULT="mir_fbar.scl")
MIRFPFMFILE yy.scl Output file with Fnat, sig, and (F+,sigma,F-,sigma)
for each derivative will be yy.scl
(DEFAULT="mir_fpfm.scl")