GroEl example file : go.URO.minimize

#!/bin/sh 
#FILE:    go.URO.minimize
#AUTHOR:  Karsten Suhre
#DATE:    Mon Jun  7 16:02:31 CEST 2004
#PURPOSE: run URO on a single model in a subdirectory
#         all computation will be done in a ./RUN.minimize
#BUGS:    
#MODIF:   

# the name of the PDB file
pdb=1aonA.pdb

# the EM map
map=GroEl.ezd

# global parameters
NMAX=25      # maximum number of iterations of URO fitting
MAXRES=400.0 # resolution range
MINRES=15.0  # resolution range

O=on # set this variable to 'on' to generate O views 
     # (may be set to 'off' to speed up the minimization a bit,
     #  but in this case, no final PDB file will be produced - run go.O by hand)

# the NMA perturbed PDB file
base=`basename $pdb .pdb`
fic1=./d/$base.NMApert.pdb

# the work directory
rundir=RUN.minimize

# test the presence of required files
if [ ! -f $fic1 ] ; then
  echo "file $fic1 not found"
  exit 1
fi

if [ ! -d ./d/. ] ; then
  echo "run amore_setup first"
  exit 1
fi

# make run directory and copy URO files 
[ -d $rundir ] && rm -r -f $rundir
mkdir $rundir
cp $fic1 $rundir
cd $rundir
cp -r ../e .
mkdir i
mkdir f
mkdir d
mkdir o

# print the run parameters
cat > params < ./d/data.d < ./i/dato.i3 < ./d/xyz1.d
egrep '^ATOM' `basename $fic1`  >> ./d/xyz1.d


# check if all files are there and if they are correct
if [ ! -f ./d/emap.d ] ; then
  echo "ERROR: no file emap.d"
  exit 1
fi
if [ ! -f ./d/xyz1.d ] ; then
  echo "ERROR: no file xyz1.d"
  exit 1
fi
if [ ! -f ./d/data.d ] ; then
  echo "ERROR: no file data.d"
  exit 1
fi

# Fourier transform of the EM box:
echo "Fourier transform of the EM box"
e/emft  d/emap.d  1 > emft.log

# Molecular scattering factors of each of the search models:

echo "Molecular scattering factors of each of the search models"
e/scat 1 > scat1.log

# Initial positional variables of the independent molecules:

echo "copying initial positions to local dir"
cp `basename $fic1` Aa.pdb || exit 1

echo "generating modlist"
cat > modlist < fit.log
FUNC=`cat fit.log | grep 'scale, correlation coefficients, r-fact, b-factor. function' | tail -1 | sed 's/.*= *//' | sed 's/\.//'`
echo "FUNC*1000 = $FUNC"

# iteration
N=1
tail -1 o/f$N.s >convergence.txt
while [ $N -le $NMAX ] ; do


         e/oic f$N fit
         N=`expr $N + 1`

         e/fiting fit f$N > fit.log
         FUNC1=`cat fit.log | grep 'scale, correlation coefficients, r-fact, b-factor. function' | tail -1 | sed 's/.*= *//' | sed 's/\.//'`
         echo "FUNC*1000 = $FUNC1"

         # test if convergence was reached
         NLAST=$N
         if [ $FUNC1 -ge $FUNC ] ; then
           N=9999
         else
           tail -1 o/f$N.s >>convergence.txt
           FUNC=$FUNC1
         fi

done

echo "$FUNC" > ../func.out

# generate final coordinates
if [ "$O" = "on" ] ; then
  # Generation of optimized coordinates:
  echo "Generation of optimized coordinates"
  e/pv2c f$NLAST
  
  # generate a file ono for visual inspection
  echo "generate a file for ono"
  ../go.O

  # para recuperar gs.real hacer:
  # write .gs_real
  # > gs.real [RETURN]
  echo "copy initial O view"
  cp ../d/gs.real .

fi

echo "URO finished, here is the convergence ..."
cat convergence.txt

• K. Suhre, J. Navaza & Y.H. Sanejouand (2006), NORMA: a tool for flexible fitting of high resolution protein structures into low resolution electron microscopy derived density maps, Acta Cryst. D, vol.62(9), p1098-1100.