# Edit this line to be your xplor data processing directory
# cd /usr/people/tutor##/exercise2
#
# Copy your model into the starting 'standard' file
#
cp model-01.pdb native.pdb
#
printf ' ********************************************************** \n'
printf ' Generate psf STRUCTURE file \n'
printf ' Generate bonds \n'
printf ' Input: native.pdb \n'
printf ' Output: generate.pdb generate.psf \n'
printf ' ********************************************************** \n'
xplor<  generate.inp |tee generate.logM01
#
cp  generate.pdb brefinement.pdb
#
printf ' ********************************************************** \n'
printf ' Positional 8 - 1.8 A \n'
printf ' Input: brefinement.pdb xplor.fob generate.psf cell.inp \n'
printf ' Output: positional.pdb \n'
printf ' ********************************************************** \n'
xplor <  posit-18.inp |tee posit-18.logM01 
#
printf ' ********************************************************** \n'
printf ' Individual B refinement 1.8 A\n'
printf ' Input: positional.pdb xplor.fob generate.psf cell.inp \n'
printf ' Output: brefinement.pdb \n'
printf ' ********************************************************** \n'
xplor <  bref-18.inp |tee bref-18.logM01 
#
printf ' ********************************************************** \n'
printf ' Positional 8 - 1.8 A \n'
printf ' Input: brefinement.pdb xplor.fob generate.psf cell.inp \n'
printf ' Output: positional.pdb \n'
printf ' ********************************************************** \n'
xplor <  posit-18.inp |tee posit-18.logM01 
#
#
printf ' ********************************************************** \n'
printf ' Individual B refinement \n'
printf ' Input: positional.pdb xplor.fob generate.psf cell.inp \n'
printf ' Output: brefinement.pdb \n'
printf ' ********************************************************** \n'
xplor <  bref-18.inp |tee bref-18_1.logM01 
#
printf ' ********************************************************** \n'
printf ' Positional 8 - 1.8 A \n'
printf ' Input: brefinement.pdb xplor.fob generate.psf cell.inp \n'
printf ' Output: positional.pdb \n'
printf ' ********************************************************** \n'
xplor <  posit-18.inp |tee posit-18_1.logM01 
#
printf ' ********************************************************** \n'
printf ' Individual B refinement \n'
printf ' Input: positional.pdb xplor.fob generate.psf cell.inp \n'
printf ' Output: brefinement.pdb \n'
printf ' ********************************************************** \n'
xplor <  bref-18.inp |tee bref-18_2.logM01 
#
printf ' ********************************************************** \n'
printf ' Positional 8 - 1.8 A \n'
printf ' Input: brefinement.pdb xplor.fob generate.psf cell.inp \n'
printf ' Output: positional.pdb \n'
printf ' ********************************************************** \n'
xplor <  posit-18.inp |tee posit-18_2.logM01 
#
printf ' ********************************************************** \n'
printf ' Individual B refinement \n'
printf ' Input: positional.pdb xplor.fob generate.psf cell.inp \n'
printf ' Output: brefinement.pdb \n'
printf ' ********************************************************** \n'
xplor <  bref-18.inp |tee bref-18_3.logM01 
#
printf ' ********************************************************** \n'
printf ' Positional 8 - 1.8 A \n'
printf ' Input: brefinement.pdb xplor.fob generate.psf cell.inp \n'
printf ' Output: positional.pdb \n'
printf ' ********************************************************** \n'
xplor <  posit-18.inp |tee posit-18_3.logM01 
#
printf ' ********************************************************** \n'
printf ' DONE: \n'
printf ' ********************************************************** \n'