vmd_read_pdb_ss 1.1

REQUIREMENTS: VMD Version 1.0 or better

	Normally VMD uses the program STRIDE in order to determine the
	secondary structure of molecules.  STRIDE uses standard algorithms,
	but its conclusions may on occasion differ slightly from
	what you expect.  This script forces VMD to assign secondary
	structure based on data in the appropriate record of the PDB file.
	Thus you can fill in this record to obtain the desired secondary
	structure representation.  To use this routine, you must
	call vmd_use_pdb_ss with both the id of the molecule to define
	secondary structure on and the file where the SS information can
	be found.

	vmd_read_pdb_ss -- extracts appropriate fields of a given PDB file
	vmd_use_pdb_ss -- determines the molecule to which a secondary
	      structure definition is to be applied, as well as the PDB
	      file from which records for the secondary structure are
	      to be obtained via vmd_read_pdb_ss

	Suppose the PDB file corresponding to the top molecule is called
	PLV.PDB.  It is assumed that this PDB file has secondary structure
	information contained within it.  Then the following command
	will define secondary structure according to this information
		vmd_use_pdb_ss top PLV.PDB
	If you choose 'Cartoon' as a representation, you will see that
	the secondary structure has been taken from the PDB file.


	Andrew Dalke (dalke@ks.uiuc.edu)