When you start VMD, the VMD text console uses the Tcl command interpreter
to process what you type. In order to use the Python interpreter, you have
to tell VMD to switch to 'Python mode'. To do this, simply type 'gopython'
in the console window. If VMD prints an error message reporting that the
Python interpreter is not available, your version of VMD was not compiled
with Python support; contact the VMD developers for help. If all goes well,
you should see Python command prompt '
' in the console window. To
switch back to the Tcl interpreter, press Ctrl-D as though you were exiting
Python. Switching back and forth between Python and Tcl does not destroy any
of your work; all variables and modules will still be defined until you exit
VMD.
Typing 'gopython 
filename
', where filename is the name of a file
containing Python code will cause VMD to switch to Python mode, process the
file, then switch back to Tcl. In this way, you can embed Python functions
inside your Tcl scripts!
You can also type 'gopython -command "your code here" to run an arbitrary line of python code.