#!/bin/csh
#
#  set CCP4 and SOLVETMPDIR variables:
#
setenv CCP4_OPEN UNKNOWN
setenv SOLVETMPDIR /var/tmp
setenv SYMINFO /usr/local/lib/solve/syminfo.lib
setenv SYMOP /usr/local/lib/solve/symop.lib
#
#
solve_giant <<EOD > solve.log

!command file to read in raw MAD data, scale, analyze and solve it----
title armadillo repeat of beta catenin 4-wavelength MAD data
logfile mad.logfile            ! write out most information to this file.
                               ! summary info will be written to "solve.prt"
@solve.setup                   ! get our standard information read in 
readformatted                   ! or: readdenzo, readtrek, readccp4_unmerged
unmerged                        ! or; premerged

mad_atom se 

refscattfactors               ! do not refine scattering factors (you can if
                              ! you want though)

        !  Comment out next line if you don't know any sites
checksolve                    ! compare solutions to the one input below

lambda 1                      ! info on wavelength #1 follows 
label Wavelength #  1         ! a label for this wavelength
rawmadfile l1.int
wavelength 0.9000             ! wavelength value
fprimv_mad  -1.6              ! f' value at this wavelength
fprprv_mad  3.4               ! f" value at this wavelength

! list of all SE positions in refined beta-catenin
! structure (offset by 0.5 in y from PDB file)

atomname se 
xyz  0.2631041      0.6633824      2.8978506E-02
xyz  0.4166300      0.6113137      7.7325497E-03
xyz  0.4765674      0.7249608      2.5320712E-02
xyz  0.4591554      0.7427059      0.4719517    
xyz  0.4083922      0.7455686      0.1403100    
xyz  0.4416372      0.8393628      7.6342024E-02
xyz  0.1327285      0.4970000      0.4364171    
xyz  9.6379094E-02  0.5855882      0.3802352    
xyz  7.6066948E-02  0.6245000      0.3974865    
xyz  0.1150683      0.7795883      0.3715025    
xyz  0.1385160      0.7238529      0.4098982    
xyz  9.2073016E-02  0.7063529      0.4022779    
xyz  0.2152710      0.8265882      0.3764597    
xyz  0.3304202      0.6161765      0.2311389    
xyz  0.1806852      0.8512745      0.1618233    

lambda 2
rawmadfile l2.int
wavelength 0.9794
fprimv_mad  -11.44
fprprv_mad  8.74

lambda 3
rawmadfile l3.int
wavelength 0.9797
fprimv_mad  -12.83
fprprv_mad  2.56

lambda 4
rawmadfile l4.int
wavelength 0.9897
fprimv_mad -2.42
fprprv_mad 1.13

nres 700                  [approx # of residues in protein molecule]
nanomalous 15              [approx # of anomalously scattering atoms per protein]
acceptance 0.10
SCALE_MAD                 ! read in and localscale the data
ANALYZE_MAD               ! run MADMRG and MADBST and analyze all the Pattersons
SOLVE                     ! Solve the structure
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_giant << EOD > resolve.log 
!solvent_content 0.40        !    solvent fraction 
seq_file weis.seq
compare_file coords_met.pdb
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.'