SCALE_MAD: Scaling MAD datasets
SCALE_MAD is a routine to read in MAD data from a Scalepack output file or from another formatted file and to scale it and put it all in a file suitable for ANALYZE_MAD and SOLVE. It is ordinarily called as the first step in a completely automated structure determination and is followed by ANALYZE_MAD and SOLVE. It can also be run on its own. The routine works well when the MAD data has been collected in very nearly the same way at all wavelengths and anomalous differences have been measured at all wavelengths either by inverse beam or by mirror plane symmetry. The routine assumes 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.
SCALE_MAD first estimates the overall absolute scale of the data using the data in the lowest resolution shell from the first datafile and the number of protein residues in the asymmetric unit (NRES). SCALE_MAD separates Bijvoet pairs into separate files. SCALE_MAD scales all the input data files to the first data file using just an overall scale and B. Then it merges all the data from all datafiles into one averaged dataset and rescales all the datasets to the averaged dataset using LOCALSCALE.
A typical input script for SCALE_MAD looks just like the one for automated MAD structure determination except you leave off the commands "ANALYZE_MAD" and "SOLVE".
KEYWORDS for SCALE_MAD:
LAMBDA n The next RAWMADFILE(s) that are read in will be
for lambda n
MADFBARFILE xx.scl Output file with (Fbar,sigma,DelAno,sigma)
for each wavelength will be xx.scl
(DEFAULT="mad_fbar.scl")
MADFPFMFILE yy.scl Output file with (F+,sigma,F-,sigma) for each
wavelength will be yy.scl
(DEFAULT="mad_fpfm.scl")
KEEPFIRSTCYCLE 1 On first cycle of scale_mad, do not reject any reflections
RATIO_OUT 3.0 Reject reflections with iso or ano diff > ratio_out*rms diff in shell
REQUIRE_NAT If native is missing, toss derivative too
ID_SCALE_REF 2 Use wavelength 2 as reference in scaling (default=1)
See also the commonly-used keywords for automated SOLVE operation.