#!/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
! 
!   Take mad and mir datasets that may or may not
!   be exactly isomorphous, combine them into one pseudo-mir dataset
!   and solve it
!
logfile solve.logfile  ! another log file

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


mad_atom se   ! define the anomalously-scattering atom

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

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----------

EOD
#
# Now run Resolve to do density modification
#
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
#
echo 'All done.'