#!/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 a MAD dataset
#
solve<<EOD > solve.log
logfile solve.logfile  

resolution 20 3.0
cell 60 60 50 90 90 90
symfile /usr/local/lib/solve/p21212.sym


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

mad_atom se     ! the anomalously-scattering atom
lambda 1
label set 1 with 2 se atoms, lambda 1
wavelength .9782                        ! wavelength value
fprimv_mad  -9                          ! f' value at this wavelength
fprprv_mad  3.5                         ! f doubleprime value
rawmadfile lam1.intensities             ! datafile for this wavelength
lambda 2
wavelength 0.977865
fprimv_mad  -8
fprprv_mad  4.5 
rawmadfile lam2.intensities

lambda 3
wavelength 0.8856
fprimv_mad  -2.5
fprprv_mad  3.0
rawmadfile lam3.intensities
nres 80                      ! number of residues in au
nanomalous 2                 ! number of anomalously-scattering atoms in au
!
scale_mad
analyze_mad
solve
EOD
#
# Now run Resolve to do density modification and build a model
#
resolve << EOD > resolve.log 
!solvent_content 0.70        !    solvent fraction 
seq_file seq.dat            !    sequence file
EOD
#
#  That's it! Now resolve.mtz has your updated phases
#  and resolve.pdb has your model
#