The above figure consists of E. coli enterotoxin (protein as spheres)
binding to GM1 pentasaccharide (sugars represented as rods)
protruding from cell membrane (plane)

It was made using the following series of commands (For Dec Alpha's. Linux and SGI's ):

Attach atom colouring to front of a PDB file (LT.pdb) containing the coordinates for the protein atoms.

cat /srv/local/raster3d/raster3d_2.5c/examples/chaincolours.pdb /srv/local/raster3d/raster3d_2.5c/examples/LT.pdb > temp.tmp

Make a space-filling representation of protein atoms 

       balls -h < temp.tmp > balls.r3d

Draw oligosaccharide as stick model 

       cat /srv/local/raster3d/raster3d_2.5c/examples/sugarcolours.pdb /srv/local/raster3d/raster3d_2.5c/examples/sugars.pdb > temp.tmp
       rods  -h < temp.tmp > sugars.r3d

Combine protein description with sugar description and add in description of plane surface lying below both.
At the front goes a file containing the header records describing the view angle, image size, lighting, etc. 

       cat /srv/local/raster3d/raster3d_2.5c/examples/header2.r3d /srv/local/raster3d/raster3d_2.5c/examples/plane.r3d sugars.r3d balls.r3d > temp.tmp

Feed the composite description through the rendering progran and pipe the output to the ImageMagick display utility.

        render -sgi example1.rgb < temp.tmp
	xv example1.rgb &

If you prefer the SGI libimage version instead, then use

       render example1.rgb < temp.tmp; ipaste example1.rgb

Clean up before leaving

       rm -f temp.tmp balls.r3d sugars.r3d

xv example1.rgb &

Last Modified: Wednesday, 11-Jun-2003 10:03:41 EDT