# solve.com  -- take 1 mad datasets that has 2 
# anomalously-scattering atoms and convert it into into one 
# pseudo-mir dataset solve it


# CCP4_OPEN environmental variable set to UNKNOWN so file overwriting will work
setenv CCP4_OPEN UNKNOWN

solve <<***
! Solve 1 mad dataset with 2 anomalously-scattering atoms

title  5-wavelength 2-ano scatterer MAD dataset   !  a title for this dataset
@solve.setup                   ! get our standard information read in 
logfile solve.logfile          ! write out most information to this file.

readformatted                  ! alternatives are readdenzo, readtrek
premerged                      ! alternative is unmerged
read_intensities               ! alternative is read_amplitudes
fixscattfactors                ! do not refine them with 2 ano atoms 

! Read in the data twice: once treated as Se and once as Fe.



mad_atom se                   ! the anomalously scattering atom is selenium
lambda 1                      ! info on wavelength #1 follows 
label Wavelength #  1         ! a label for this wavelength
rawmadfile lam1.intensities   ! datafile for lambda 1 containing raw Intensities 

wavelength 0.9000             ! wavelength value
fprimv_mad  -1.6              ! f' value at this wavelength (for Se)
fprprv_mad  3.4               ! f doubleprime value at this wavelength

atomname se                   ! about to enter data on an atom


lambda 2
rawmadfile lam2.intensities
wavelength 0.9794
fprimv_mad  -8.5
fprprv_mad  4.8

lambda 3
rawmadfile lam3.intensities
wavelength 0.9797
fprimv_mad  -9.85
fprprv_mad  2.86

nres 100                  [approx # of residues of protein in asymmetric unit]
nanomalous 1              [approx # of anomalously scattering Se atoms in a.u.]
SCALE_MAD                 ! read in and localscale the data
ANALYZE_MAD               ! run MADMRG and MADBST and analyze all the Pattersons

! now do it all over for Fe instead of Se:

NEW_DATASET                   ! tell solve we're starting a new dataset

mad_atom Fe                   ! the anomalously scattering atom is Fe 

lambda 1                      ! info on wavelength #1 follows 
label Wavelength #  1         ! a label for this wavelength
rawmadfile lam4.intensities   ! datafile for lambda 1 containing raw Intensities
atomname fe 

wavelength 1.74             ! wavelength value
fprimv_mad  -9              ! f' value for Fe at this wavelength
fprprv_mad  2.5             ! f doubleprime at this wavelength

lambda 2
rawmadfile lam5.intensities
wavelength 1.73647
fprimv_mad  -5
fprprv_mad  4.5

lambda 3
rawmadfile lam3.intensities
wavelength 0.9797
fprimv_mad 0.3 
fprprv_mad  1.5

nres 100                  [approx # of residues of protein in asymmetric unit]
nanomalous 1              [approx # of anomalously scattering Fe atoms in a.u.]
SCALE_MAD                 ! read in and localscale the data
ANALYZE_MAD               ! run MADMRG and MADBST and analyze all the Pattersons

! now combine the datasets into one

COMBINE_ALL_DATA

! now solve it as a whole

SOLVE                     ! Solve the structure

!--------all done----------

***