Unialign

Usage Manual

You can specify options or commands through the command line. You can also run the program in an interactive mode where you can type commands. The command line format is as follows:

unialign.exe "option1 value1" "option2 value2" "command1" "command2 argument2 argument3" ...

Equivalently, you can type the same commands in interactive mode:

unialign.exe "cmdmode 1"
> option1 value1
> option2 value2
> command1
> command2 argument2 argument3

Available Options and Commands

command	description
help	print options and their current values
cmdmode [0	1]	run in interactive mode – only effective if provided in command line
(q)uit	exit the program
datadir /path/to/datadir	set the data directory where the pdb files reside
align pdbfile1 pdbfile2	align two protein structures