#!/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
#
#  command file to solve a 2-deriv MIR dataset + anom diffs in native
#
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 lam1.intensities ! native data

! now read in native data again as a pseudo-deriv 1:
! put in scattering factors for pseudo-atom fel1 with only ano
! scattering

newatomtype FEL1
aval 0 0 0 0
bval 0 0 0 0
cval 0.001
fprimv 0 
fprprv 3

derivative 1
label native data with ano diffs, treated as deriv 1
nsolsite_deriv 1               ! just 1 site
rawderivfile lam1.intensities
inano
anoonly                        ! no isomorphous diffs, just ano
atomname fel1                  ! use our pseudo-atom with no iso scattering

! now read in the regular 2 derivs:
derivative 2                   ! about to enter information on derivative #1
label deriv 1 HG               ! a label for this deriv
nsolsite_deriv 1               ! one site in this deriv
rawderivfile der1.intensities  ! data from generate.com
inano                          ! You need to tell it if anomalous diffs are
                               ! to be used
noanorefine                     ! do not use ano diffs for refinement 
atomname Hg                   ! tell SOLVE what the heavy atom is

derivative 3
label deriv 2 also hg
rawderivfile der2.intensities        ! the derivative data is in this file
nsolsite_deriv 2
inano
noanorefine                     ! do not use ano diffs for refinement 
atomname hg
acceptance 0.35                 ! accept a new site if it has a
                                ! peak height about 1/3 of avg or more
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 0.4        !    solvent fraction 
EOD
#
#  That's it! Now resolve.mtz has your updated phases
#  and resolve.pdb has your model
#