#!/bin/csh
#
#  set CCP4 and SOLVETMPDIR variables:
#
setenv CCP4_OPEN UNKNOWN
setenv SOLVETMPDIR /var/tmp
setenv SYMINFO /usr/local/lib/solve/syminfo.lib
setenv SYMOP /usr/local/lib/solve/symop.lib
#
solve <<EOD > solve.log
!command file to read in raw MAD data, scale, analyze and solve it----
checksolve                     ! compare solution with known h.a. sites
@solve.setup                   ! get our standard information read in 
logfile mad.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
refscattfactors                ! alternative is fixscattfactors


mad_atomname se                ! anomalously scattering atom is Se

lambda 1                      ! info on wavelength #1 follows 
label Wavelength #  1         ! a label for this wavelength
rawmadfile test_wva.fmt       ! datafile with h k l Intensity sigma or
                              ! h k l I+ sigma+ I- sigma-
wavelength 0.9000             ! wavelength value
fprimv_mad  -1.6              ! f' value at this wavelength
fprprv_mad  3.4               ! f doubleprime value at this wavelength

! input refined h.a. coordinates (used only for comparison in "checksolve")
! offset by 1/2 in y to match gvp.pdb 2-27-01. 
atomname se
 XYZ   0.4813319      0.4972169      9.4140753E-02 
 XYZ   0.9731338      0.7875228      0.9446641

lambda 2
rawmadfile test_wvb.fmt
wavelength 0.9794
fprimv_mad  -8.5
fprprv_mad  4.8

lambda 3
rawmadfile test_wvc.fmt
wavelength 0.9797
fprimv_mad  -9.85
fprprv_mad  2.86
premerged                  
readformatted
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
SOLVE                     ! Solve the structure
EOD
#
# Now run Resolve to do density modification
# (You can download it from http://resolve.lanl.gov 
# if you do not have it yet) 
#
resolve << EOD > resolve.log 
!solvent_content 0.40        !    solvent fraction 
seq_file gvp.seq
compare_file coords.pdb
EOD
#
#  That's it! Now resolve.mtz has your updated phases
#
echo 'Here are your SOLVE and resolve files:' 
#
ls -l solve.prt solve.mtz solve.ezd resolve.mtz
#
echo 'All done.'