#!/bin/bash
#
# Calculate molecular surface of a galactose molecule using MSMS
#
ln -s ../sugarG.pdb protein.pdb
cat protein.pdb | pdb_to_xyzr > surf.dat
msms -if surf.dat -of surf -probe_radius 1.4 -density 5.0
#
#
# Convert the msms output into a Raster3D description of the surface
#
./msms2r3d.pl surf.face surf.vert > surf.r3d
#
#
# Use rastep to make an auto-centered ball+stick view of the molecule
#
rastep -auto -rad 0.20 -prob 0.10 < protein.pdb > protein.r3d
#
# Combine the ball+stick figure with a transparent material 
# description from the Raster3D library 
# applied to the molecular surface generated in MSMS
# Save the combined picture as a TIFF file
#
render -size 800x800 -zoom 75% -transparent -tiff picture.tiff << EOF
@protein.r3d
@translucent_60
@surf.r3d
EOF
#
rm -f protein.pdb msms_surf.dat.log
rm -f surf.dat surf.face surf.vert
rm -f surf.r3d
rm -f protein.r3d
display -geometry 50% picture.tiff&
