This directory hold a program called convert which
changes one side chain for another from a given set.

The program needs a single line file called $1.num
to tell it what to do. The one line of this file
must contain four integers. The first is the MacroModel
number of the atom to be the alpha atom - that is the atom
that will be unchanged to which the side chain is joined.

The second number is the MM number of the first atom of 
the side chain.

The third number is the option corresponding to the 
desired side chain.

The fourth number is either 0 or 1.
If it is 1, the program will find the structure in which
the new sidechain has the greatest shortest interatomic
distance.  If it is 0 it won't!  This number must be 
included even if it is to be 0.

The input file is $1.dat
The output file is $1.con

The file sdchns.dat must be copied into the directory
from which the program is being run.

When the .dat and .num files are set up, type

convert $1

Sidechains:

Option	Description

1  	Hydrogen
2	Methyl
3	Hydroxy
4  	Phenyl
5	Cyclohexyl (equatorial connection)
6	Cyclohexyl (axial connection)
7	Ethyl
8	Trimethylsilyl
9	tButyldimethylsilyl


Setting up new sidechains:

Create new structure in MacroModel with the new alpha
atom as atom number 1 and the beta as atom number 2.

Minimize.

Delete all other atoms connected to the new alpha atom.

Save structure.

Jot structure file.

Remove the title.

Copy the contents of the structure file to the bottom of the file
SDCHNS.DAT.

Go to the top of SDCHNS.DAT - the first number is the total
number of sidechains available.  Increase this by one - this 
number is that of the new sidechain option.

Add new option to the README file.

