Getting Started

I generally start by using molauto (part of Molscript) to generate a ribbon diagram. I have a script that:

• Converts selenomethionines (MSE) into methionines (MET).
• Uses dssp to calculate the secondary structure and add SHEET and HELIX lines to the top of your pdb.
• Runs molauto
• Edits the molauto output to make it a little prettier (color the inside of helicies, make the background white, etc)
• Adds a rotatable unit cell.

•      [dcoop molscript]-> molauto myfile.pdb > ribbon.ms

  Then I get a view close to what I want using Rasmol

       [dcoop molscript]-> rasmol myfile.pdb
       RasMol> rotate and translate with the mouse 
       RasMol> write molscript temp
       RasMol> quit

  Take the orientation statements from the Rasmol output and put it in the Molauto output

       [dcoop molscript]-> head -15 temp
       ! File: temp
       ! Creator: RasMol Version 2.7.1
       ! Version: MolScript v1.3
       
       plot
         window 26.3084;
       
         read mol "mona.pdb";
         transform atom *
         by centre position atom *
         by rotation x 180.0                  |   Take
         by rotation z -45.0804               |   These
         by rotation y -59.3008               |   Lines
         by rotation x -99.9908               |
         by translation -3.19720 3.88231 0.0; |
  

  Then I use the opengl mode (molscript -gl -in ribbon.ms) re-read input file function) until I get the file to look like I like. Write out the orientation and ADD IT BELOW the by translation line (but before the semicolon ; ).

  Then I use this script to run the molscript file through render.

  Improving Molauto
  Vi command to add plane2color statements to molauto lines.
  :1,$ s/hsb \(.*\) 1 1;/hsb \1 1 1, plane2colour hsb \1 .7 .7;

  If you don't like vi:
  sed 's/ hsb \(.*\) 1 1;/hsb \1 1 1, plane2colour hsb \1 .7 .7' infile > out

  The difference is between this and that.