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://dev.scriptics.com/). 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 ($) sign to indicate there characters needed to define a command. You can also get a list of all available commands by typing the question (?) mark at the command prompt. Very many of the commands return a parameter (or several) which can be used as an input to a new command.
Please observe that when using the commands in scripts one needs to fill in the full command name!
Commands available: atom define various properties about atoms calc$ulate calculate molecular properties cent$er center the system on the screen conto$ur display and define isosurface plots defi$ne define general properties displ$ay display the current picture edit edit molecule and molecule properties expo$rt export molecular structures fill fill time series vectors find find/calculate various things gomError "text" print the "text" through the ERROR module gomPrint "text" print the "text" through the Print module gscal$e scale the current display hard$copy make a hardcopy of the currecnt display help help system impo$rt import molecular coordinates and other things mani$pulate manipulate time series moni$tor monitor molecular properties from a trajectory mope$n open old model file msav$e save model file pause Fvalue pause for Fvalue seconds plot plot various things plum$ber plot a ribbon or tube through atoms ptra$ce trace atoms through the trajectory quit stop program and exit rese$t reset the system rota$te rotate the current display run run various programs sele$ct make a selection from the current atoms show show various things traj$ectory trajectory display and analysis control tran$slate translate the current display wind$ow window operations
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 ************************************************************************** LUL/1996 **************************************************************************