# solve.com  -- take mad and mir datasets that may or may not
#   be exactly isomorphous, combine them into one pseudo-mir dataset
# and solve it

# CCP4_OPEN environmental variable set to UNKNOWN so file overwriting will work
setenv CCP4_OPEN UNKNOWN
solve <<***
@solve.setup                   ! get our standard information read in
logfile mir.logfile            ! write out most information to this file.
                               ! summary info will be written to solve.prt

readformatted                  ! alternatives are readdenzo, readtrek
premerged                      ! alternative is unmerged
read_intensities               ! alternative is read_amplitudes
!
!---------MAD dataset (se atoms)---------
mad_atom se
fixscattfactors
lambda 1
label set 1 with 2 se atoms, lambda 1
wavelength .9782                      ! wavelength value
fprimv_mad  -10                       ! f' value at this wavelength
fprprv_mad  3                         ! f doubleprime
rawmadfile lam1.intensities           ! data file
ATOMNAME Se

lambda 2
wavelength 0.977865
fprimv_mad  -7.5
fprprv_mad  5
rawmadfile lam2.intensities

lambda 3
wavelength 0.8856
fprimv_mad  -2
fprprv_mad  3.5
rawmadfile lam3.intensities
nres 100                  [approx # of residues in protein molecule]
nanomalous 2              [approx # of anomalously scattering atoms per protein]
SCALE_MAD                 ! read in and localscale the data
ANALYZE_MAD               ! run MADMRG and MADBST and analyze all the Pattersons

!------------------------end of first dataset -------------

new_dataset

!----------------second dataset (MIR with Pt atoms) ----------
rawnativefile native.intensities
!
derivative 1
label set 1 with 1  pt atoms, deriv 1
rawderivfile der1.intensities
atomname pt

nsolsite 1
scale_native
scale_mir
analyze_mir
!--------------------------end of second dataset --------------

!  combine the datasets into one now...

combine

!------ go -------
solve
!--------all done----------

***