16 Advanced Script Writing

 

The biggest improvement in VMD 1.1 has been the addition of commands for analyzing atomic and molecular information. This chapter describes through examples how to put those commands together to write scripts. We assume at this point you already read through the other chapters which describe the various commands, including:

• how to use Tcl (see Chapter §)
• which commands are/are not ``core'' commands (see section §)
• the Tcl vector and matrix extensions (see Chapter §)
• the atomselect, molinfo, and colinfo commands (see Chapter §  and section §)

The examples used will not be described in detail, but will only explain some of the more unusual or novel features of the VMD scripting language. The source of the examples can be found in the VMD script library at http://www.ks.uiuc.edu/Research/vmd/script_library/.

Many of these scripts use the trace command from Tcl. This does not mean all good scripts must use that command, but rather that putting a trace on a variable is a nice way to add an automatic action.

 
• 16.1 Drawing a distance matrix
• 16.2 Analysis of PDB files
• 16.3 save/load VMD state information
• 16.4 Currently picked molecule/atom
• 16.5 Trace on the pick variables
  • 16.5.1 Information about the picked atom
  • 16.5.2 Making a sphere appear when an atom is picked
  • 16.5.3 Drawing a line from the eye to the picked atom
• 16.6 Trajectory frames
  • 16.6.1 Animating the secondary structure
  • 16.6.2 Viewing selections which change during an animation
  • 16.6.3 Simulation frames
• 16.7 RMSD and best-fit alignments
  • 16.7.1 RMSD Computation
  • 16.7.2 Computing the Alignment
  • 16.7.3 A simulation example script