#!/bin/csh
#
#  set CCP4 and SOLVETMPDIR variables:
#
setenv CCP4_OPEN UNKNOWN
setenv SOLVETMPDIR /var/tmp
setenv SYMOP /usr/local/lib/resolve/symop.lib
#
#  mad_mir_dataset.com
# 
#   Take mad and mir datasets that may or may not
#   be exactly isomorphous, combine them into one pseudo-mir dataset
#   and solve it
#
solve <<EOD > solve.log
@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                  ! or: readdenzo, readtrek, readccp4_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 lambda_1.fft    ! compare FFT to perfect one in lambda_1.fft
!
!---------MAD dataset (se atoms)---------
mad_atom se
fixscattfactors
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
ATOMNAME Se
xyz  0.44 0.16 0.38                   ! coordinates (comparison only)
xyz  0.23 0.45 0.165                  ! comment out if unknown
xyz 0.18 0.53 0.77  


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
xyz 0.18 0.53 0.77                  ! coords; comparison only

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
# (You can download it from http://resolve.lanl.gov 
# if you do not have it yet) 
#
resolve << EOD > resolve.log 
solvent_content 0.4        !    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.'