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           This is the main help level for the gOpenMol program
                        Leif Laaksonen CSC 2002
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The command line parser is implemented using the Tcl (Tool command language).
The language is rich of commands and I strongly recommend you first to have
a look the the Tcl commands (http://www.sunlabs.com:80/research/tcl/).

For most commands it is enough just to use the four first characters
to uniquely define the command. A clear exception is the 'contour'
command where the first five characters are needed not to mix the
command with the 'continue' statement. Through the help files I have
used a dollar ($) sign to indicate there characters needed to define a
command. You can also get a list of all available commands by typing
the question (?) mark at the command prompt.

Very many of the commands return a parameter (or several) which can be
used as an input to a new command.

Commands available:

atom               define various properties about atoms    
calc$ulate         calculate molecular properties
cent$er            center the system by choosing atoms
conto$ur           display and define isisurface plots
defi$ne            define general properties
displ$ay           display the current picture
edit               edit molecule and molecule properties
expo$rt            export molecular structures
fill               fill time series vectors
hard$copy          make a hardcopy of the currecnt display
help               help system
impo$rt            import molecular coordinates and other things
moni$tor           monitor molecular properties from a trajectory
mope$n             open old model file
msav$e             save model file
plot               plot various things
plum$ber           plot a ribbon or tube through atoms
rese$t             reset the system
rota$te            rotate the current display
gscal$e            scale the current display
sele$ct            make a selection from the current atoms
show               show various things
trac$e             trace atoms through the trajectory
traj$ectory        trajectory display and analysis control
tran$slate         translate the current display

You don't always need the graphics when you use gOpenMol. In fact in
some cases it's an advantage not to use the graphics. The command
line options when you start gOpenMol are:

    gopenmol -cInputCoord.Ext -h -t -ln -mModel.gom -pFile.Name  
                                                                 
    -mModel.gom start GopenMol with the model file Model.gom     
    -cInputCoord.Ext start gOpenMol with coordinate file         
    -pfile.name start gOpenMol with parameter file 'File.Name'  
    -t start gOpenMol without any graphics      
    -ln do not write a log file  (GOPENMOL.LOG) 
    -ly force the write of the log file (GOPENMOL.LOG) 
    -h print this help                                 

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LUL/2002
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