#!/bin/csh
#
#   solve.com file to run SOLVE/RESOLVE version 2.01
#
setenv SYMINFO /usr/local/lib/solve/syminfo.lib
#  set CCP4 and SOLVETMPDIR  and SYMOP variables:
#
setenv CCP4_OPEN UNKNOWN
setenv SOLVETMPDIR /var/tmp
setenv SYMOP /usr/local/lib/solve/symop.lib
setenv SYMINFO /usr/local/lib/solve/syminfo.lib
#
#   use all system resources:
#
unlimit
#
solve<<EOD > solve.log

! Solve 1 mad dataset with 2 anomalously-scattering atoms

logfile solve.logfile  

resolution 20 3.0
cell 76 28 42 90 103 90
symfile /usr/local/lib/solve/c2.sym


readformatted        ! readformatted/readdenzo/readtrek/readccp4_unmerged
premerged            ! premerged/ unmerged
read_intensities     ! read_intensities/read_amplitudes
fixscattfactors      ! fixscattfactors/refscattfactors

title  5-wavelength 2-ano scatterer MAD dataset   !  a title for this dataset

! 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                   !  the atom name

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----------

EOD
#
# Now run Resolve to do density modification and build a model
#
resolve << EOD > resolve.log 
!solvent_content 0.4        !    solvent fraction 
EOD
#
#  That's it! Now resolve.mtz has your updated phases
#  and resolve.pdb has your model
#