#!/bin/csh
#
#  set CCP4 and SOLVETMPDIR variables:
#
setenv CCP4_OPEN UNKNOWN
setenv SOLVETMPDIR /var/tmp
setenv SYMOP /usr/local/lib/resolve/symop.lib
#
#  command file to solve a 2-deriv MIR dataset
#
solve <<EOD > solve.log

!   solve a 2-deriv MIR dataset
@solve.setup                   ! get our standard information read in
logfile mir.logfile            ! write out most information to this file.
                               ! summary info will be written to solve.prt

readformatted                  ! alternatives are readdenzo, readtrek, readcp4_unmerged
premerged                      ! alternative is unmerged
read_intensities               ! alternative is read_amplitudes

        !  Comment out next line if you don't know any sites
checksolve                     ! compare sites to input sites below
        !  Comment out next line for non-model data
comparisonfile native.fft      !  compare with perfect fft for model data

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
xyz -0.620932 -0.0765346 -0.637333    ! input heavy atom sites (comparison only)
xyz -0.315098 -0.512727 -0.664318
rawderivfile der1.intensities  ! data from generate.com
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
xyz 0.620932 0.5765346 0.337333
xyz 0.515098 0.212727 0.364318

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
# (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 
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.'