# solve.com -- take 1 mad dataset and solve it
# Uses ANALYZE_SOLVE to input heavy atom sites that are known
#
# CCP4_OPEN environmental variable set to UNKNOWN so file overwriting will
work
setenv CCP4_OPEN UNKNOWN

solve <<EOD
@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
refscattfactors ! alternative is fixscattfactors

mad_atom se
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 value
rawmadfile lam1.intensities ! datafile
ATOMNAME Se ! we're about to enter data on an atom
xyz 0.44 0.16 0.38 ! coordinates of a known site
xyz 0.23 0.45 0.165 ! another site. These are to
! be used with "analyze_solve"

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 80
nanomalous 2
!
analyze_solve ! start with the sites listed above and refine them
!                   and write out phases and results
!                  note: analyze_solve must come before "analyze_mad"

scale_mad
analyze_mad
solve
!--------all done----------

EOD