This directory contains a few small utility programs which
have not been fully incorporated into PREPI as yet.

addchain
	Function: Reads a PDB file and automatically adds
		  and increments chain Labels. Useful if
		  you have a pdb file where multiple chains
		  have the same chain Label.
	Input:    PDB file
	Output:   PDB file
	Use:	  Type "addchain".Program will ask questions

colours
	Function: Simply lets you interactively play with colours
		  and their component RGB/HSI values.
	Input:    none
	Output:   none
	Use:	  Type "colours"


formatpdb
	Function: Reads a pdb file, which may not be correctly
		  formatted e.g. x,y,z in incorrect positions and
		  reformats it correctly. The input file must
		  contain 3 decimal numbers for the x,y,z
		  coordinates. Program uses these to position
		  data.
	Input:    PDB file
	Output:   PDB file
	Use:	  Type "formatpdb  input-pdb-file  output-pdb-file"

orderpdb
	Function: Reads a pdb file and puts atoms in correct
		  order (e.g. N,C,CA,O ...).
	Input:    PDB file
	Output:   PDB file
	Use:	  Type "orderpdb  input-pdb-file  output-pdb-file"


pdbarea
	Function: Calculates solvent accessible areas. For multichain
		  proteins, program can also compute area losses (i.e.
		  in going from the monomeric to oligomeric state for
		  each chain).
	Input:    pdbarea input file
	Output:   A number of files containing solvent accessible
		  areas at the atom, residue & chain levels.
	Use:	  Make a copy of the file pdbarea.inp and edit the
		  copy to your own requirements. pdbarea.inp contains 
		  further information. Then Type "pdbarea input-file".

pdbinfo
	Function: Lists a summary of PDB file contents. E.g. Number
		  of atoms, residues, start-end residue ids',...
	Input:    PDB file
	Output:   Outputs to terminal		  
	Use:	  Type "pdbinfo  input-pdb-file"
	
pi
	Function: Gives a value for Pi to many places. No use at all !
	Input:    none
	Output:   PI
	Use:	  Type "pi"

placepdb
	Function: Simple program to read a set of PDB files
		  and place them on a grid. This is a tempory
		  measure until PREPI has full multi-file input
		  capability. In PREPI the molecular positions
		  can then be fine tuned using MOVE CHAIN (under MISC)
		  Use this program generally if you need to arrange
		  a set of PDB files for plotting/visualising on a
		  grid.
		  Program can also be run as
	Input:    File containing list of PDB file names
	Output:   PDB file
	Use:	  Type "placepdb < pdb-file-list"
		  Where pdb-file-list contains a list of pdb file.
		  Program will request further information.
