#!/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.com   solve an MIR problem
#
solve<<EOD > solve.log
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

rawnativefile native.intensities ! native data H K L Iobs Sigma usually
                          ! NOTE: all datafiles must be in the same format

derivative 1                   ! about to enter information on derivative #1
label deriv 1 HG               ! a label for this deriv
atom hg

rawderivfile der1.intensities  !  derivative data
inano             ! You need to tell it if anomalous diffs are to be used
noanorefine       ! use anomalous differences in phasing
                  ! but not refinement (best option for MIR)
nsolsite_deriv 2         ! max 2 sites this deriv

derivative 2
label deriv 2 also hg
atom hg

inano
noanorefine                     ! use anomalous differences in phasing
                                ! but not refinement (best option for MIR)
rawderivfile der2.intensities        ! the derivative data is in this file


acceptance 0.35                 ! accept a new site if it has a
                                ! peak height about 1/3 of avg or more
nsolsite 2                      ! number of sites per deriv
                                ! (use nsolsite_deriv to set individual values) 
SCALE_NATIVE                    ! scale the native dataset
SCALE_MIR                       ! scale the derivs to the native
ANALYZE_MIR                     ! analyze this mir data and set up for SOLVE
SOLVE
EOD
#
# Now run Resolve to do density modification and build a model
#
resolve << EOD > resolve.log 
!solvent_content 0.40        !    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
#