#!/bin/csh
#
#    resolve_pattern.csh
#    T. Terwilliger 5-9-03
#
#   Statistical density modification using local patterns of density
#
#   Requires version 2.05 or higher of SOLVE/RESOLVE
#
#   Input file: solve.mtz or equivalent
#   Output file: solve_image.mtz  
#
#    The output file solve_image.mtz contains phase information from patterns
#    combined with solve.mtz phase information. Does not contain information
#    from solvent flattening, etc. except as transmitted through the patterns
#
#===========================================================================
#           Here are the things you might want to modify:
#===========================================================================
#
set resolution = '200 2.6'
set solvent_content = UNKNOWN   # set to "UNKNOWN" if you want resolve to guess
set input_phases = solve.mtz
set labin = 'FP=FP PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD'
set hklout = solve_image.mtz
#
setenv SOLVEDIR /usr/local/lib/solve/
setenv SOLVETMPDIR /var/tmp
unlimit
#
set resolve = /usr/local/bin/resolve
set resolve_pattern = /usr/local/bin/resolve_pattern
#
#===========================================================================
#           Normally do not edit below here
#===========================================================================
#
#
#   Procedure:  
#
#  1. begin with solve.mtz and carry out statistical density modification
#     in the usual way, including NCS, solvent flattening as appropriate.
#     result: resolve_std.mtz  (density modified phases)
#
#  2. use resolve_std.mtz phases to make a map, get patterns with 
#     resolve_patterns algorithm. Write the recovered map to 
#     recovered_map.dat.
#
#  3. Use image-based phasing in resolve with recovered_map.dat to get
#     new phase estimates based only on information from the patterns,
#     combine these phase estimates with solve.mtz phases (NOT with
#      resolve_std.mtz phase) to yield solve_image.mtz.
#
#  4. repeat steps 1-3 beginning with solve_image.mtz instead of solve.mtz
#
#
#------------------------------------------------------------------------
#
setenv SYMOP $SOLVEDIR/symop.lib
setenv CCP4_OPEN UNKNOWN
#
echo " "
echo "resolve_pattern script"
date
echo " "
if ( ! -f ${input_phases} )then
  echo "Sorry you need the file ${input_phases} for this script"
  exit
endif
#
echo "FP PHIB FOM SIGFP etc from ${input_phases}"
echo "solvent content ${solvent_content}"
echo "resolution ${resolution}"
echo " "
# set solvent content if it is known
#
if ( ${solvent_content} != 'UNKNOWN' ) then
  echo "Using solvent content of ${solvent_content} throughout"
  set find_solvent_content = 'NO'
else
  echo "Identifying optimal solvent content on first cycle"
  set find_solvent_content = 'YES'
endif
#
if ( -f ha.pdb )then
 echo "Using coordinates in ha.pdb to identify NCS if any"
endif
#
echo "Output phases (from $input_phases and image) will be in $hklout"
# run resolve on input_phases(normally solve.mtz, never density-modified phases)
#
#=====================================================================
if ( $find_solvent_content == 'NO' )then
#
#  we have solvent content...
#
echo "Running resolve on ${input_phases} with "
echo "solvent content $solvent_content to get resolve_std.mtz"
#
${resolve}<<EOD>resolve_std.log
hklin ${input_phases}
labin ${labin}
resolution ${resolution}
solvent_content  $solvent_content 
no_build
nohl
hklout resolve_std.mtz
EOD
#
else
#
#  we do not have solvent content...
echo "Running resolve on ${input_phases} to get resolve_std.mtz"
echo "Finding solvent content automatically"
#
${resolve}<<EOD>resolve_std.log
hklin ${input_phases}
labin ${labin}
resolution ${resolution}
no_build
nohl
hklout resolve_std.mtz
EOD
#
echo "Approximate solvent content is `cat resolve.solvent`"
echo " "
endif
#=====================================================================
#
cp resolve_std.mtz resolve.mtz
#
#===================================================================
foreach cycle (1 2 3 )
echo " "
echo "Cycle $cycle of pattern identification"
#
#   get recovered image from resolve map
#
${resolve_pattern}<<EOD>pattern.log
hklin resolve.mtz 
labin FP=FP PHIB=PHIM FOM=FOMM
resolution ${resolution}
recover_image
cc_map_file recovered_map.dat
EOD
#
#  combine image with solve to get solve_image
#
${resolve}<<EOD>recover.log
resolution ${resolution}
hklin ${input_phases}
labin ${labin}
no_build
pattern_phase
prior_weight 1.0
hklout ${hklout}
read_cc_map
cc_map_file recovered_map.dat
use_input_solv
use_input_db
EOD
#
echo "New cycle $cycle phases from $input_phases and images are in $hklout"
#   run resolve on this new solve_image.mtz:
#
${resolve}<<EOD>resolve_cycle.log
hklin $hklout
labin FP=FP PHIB=PHIM FOM=FOMM HLA=HLAM HLB=HLBM HLC=HLCM HLD=HLDM
resolution ${resolution}
no_build
nohl
hklout resolve_cycle.mtz
use_input_solv
use_input_db
EOD
cp resolve_cycle.mtz resolve.mtz
#
echo "End of cycle $cycle.  Current combined phases (solve+image) "
echo "are in $hklout"
end
#===================================================================