Residue Distribution 1.3
------------------------

REQUIREMENTS: VMD Version 1.1 or greater (?)

CHANGELOG:
        1.1 fixed some wrong variable names
        1.2 added parentheses around $sel1 to ensure correct function
	1.3 added parameter for output filenames prefix and changed output name

DESCRIPTION:
	Script for extracting distribution of residues of givent type 
	around selection (e.g. distribution of given type of ions around 
	protein).
	
HOW IT WORKS:
	Script goes through the defined range of distances and counts number
	of residues of specified type located within the distance of selection.
	Residues are defined by means of their name (rname) and the name of
	atom that is part of this residue and is unique in it (aname). Script 
	selects all atoms of residues of given type within the distance of 
	selection and then counts number of aname atoms. This gives the number
	of residues.
	Please make sure that your structure is imaged and centered. VMD doesn't
	support handling PBC in "within" and similar commands yet.
	See the script itself for more information.
	
PROCEDURES:
	getResDistrib - main procedure

EXAMPLE USAGE AND OUTPUT:
	usage:
	getResDistrib "sel1" "aname" "rname" min_distance max_distance step output_prefix <startframe <endframe>>
	Optional startframe/endframe parameters define range of frames from
	the trajectory, that should be analyzed. If omitted, whole trajectory
	is parsed
	
	example:
	getResDistrib "protein" "N1" "CHL" 1.0 50. 0.5 1 100 "chl"
	This analyzes average distribution of CHL residues (represented by atom N1)
	around the protein. Range of distances from 1.0 to 50.0 A will be used,
	with step 0.5 A. Only frames 1 to 100 will be parsed.
	Output goes to file output_prefix-distrib.dat (i.e. chl-distrib.dat in our case) and has
	following format
	distance	number of residues within this distance of selection
	i.e.
	1.0 0.0
	1.5 0.011
	2.0 1.492
	2.5 4.9035
	...
	49.0 35.0
	49.5 35.0
	50.0 35.0
	for system with 35 CHL residues in simulation box.

DOWNLOAD FILE:
	_res_distrib.tcl

AUTHOR:
	Lubos Vrbka (lubos (dot) vrbka (at) gmail (dot) com)