Raster3D is a rendering program that creates raster images from PDB files (3D coordinates). ImageMagick is a package used to display these render images and convert them to other formats like JPEG, GIF, POSTSCRIPT, etc.

Online manuals: Raster3D and ImageMagick

1. Setting the enviroment:

   Add the following lines to your path command in .cshrc or .tcshrc or .login:

   set path = ($path  /joule2/programs/ImageMagick /joule2/programs/Raster3D)
   

   Then source your .login or .cshrc. Alternatively you can logout and login again.

2. Test your molscript script by displaying the rendered image and change colors, size and other parameters:

   molscript -r < mol.in | render | display avs:- 
   

3. To make the final copy write out a file in GIF format:

   molscript -r < mol.in | render |  convert avs:-  mol.gif
   

4. If you want to add labels or other goodies, FTP file to Macs and using ImageConverter and/or Photoshop add Labels.

5. If you want to print directly without adding labels:

   convert mol.gif mol.ps  ; lpr -Pcolor1 mol.ps
   

1. To make a short movie:

   • Edit the molscript script file and change the rotation around the Y coordinate (add 5°) and write out new scripts.

   • Run the molscript and render to create several GIF files:

     molscript -r < er0.in | render | convert avs:- er0.gif
     molscript -r < er5.in | render | convert avs:- er5.gif
     molscript -r < er10.in | render | convert avs:- er10.gif
     molscript -r < er15.in | render | convert avs:- er15.gif
     molscript -r < er20.in | render | convert avs:- er20.gif
     

   • Make the movie:

     animate *.gif
     

     (remember to keep only the GIF files that you need in this directory)

2. To make a slide show:

   montage er0.gif er5.gif er10.gif er15.gif er20.gif allslides.gif