#!/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  -- take 2 mad datasets that may or may not
#   be exactly isomorphous, combine them into one pseudo-mir dataset
# and solve it
#
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

!
!---------first MAD dataset (se atoms)---------
mad_atom se
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 value
rawmadfile lam1_se.intensities          ! datafile
ATOMNAME Se                             ! we're about to enter data on an atom 
lambda 2
wavelength 0.977865
fprimv_mad  -7.5
fprprv_mad  5
rawmadfile lam2_se.intensities

lambda 3
wavelength 0.8856
fprimv_mad  -2
fprprv_mad  3.5
rawmadfile lam3_se.intensities
nres 80
nanomalous 2
!
scale_mad
analyze_mad

!------------------------end of first dataset -------------

new_dataset                   ! tell solve we're about to start a new one

!----------------second MAD dataset (fe atoms) ----------
mad_atom fe   
!
lambda 1
label set 1 with 1  fe atoms, lambda 1
wavelength 1.74               ! wavelength value
fprimv_mad  -9                ! f' value at this wavelength
fprprv_mad  2.5               ! f doubleprime value at this wavelength
rawmadfile lam1_fe.intensities
atomname fe

lambda 2
label Fe PK
wavelength 1.73647
fprimv_mad  -5
fprprv_mad  4.5
rawmadfile lam2_fe.intensities

lambda 3
label Fe RM
wavelength 0.978
fprimv_mad  1
fprprv_mad  1.5
rawmadfile lam3_fe.intensities
nres 80
nanomalous 1
scale_mad
analyze_mad
!--------------------------end of second dataset --------------

!  combine the datasets into one now...

combine

!  solve it...
solve
!--------all done----------

EOD
#
# Now run Resolve to do density modification and build a model
#
resolve << EOD > resolve.log 
!solvent_content 0.40        !    solvent fraction 
EOD
#
#  That's it! Now resolve.mtz has your updated phases
#  and resolve.pdb has your model