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The '''system''' command, executes a command in a subshell under Unix or Windows. # execute 'command'

...which binds a user defined function as a command into the PyMOL scripting language. * All command arguments are passed as strings to the Python function. This may require ty

...et a list of some common commands by typing "help commands" into the pymol command line. Typing this in to version 1.1r1 returns the following: LANGUAGE alias extend

Atom selections can be named for repeated use by using the select command: ...ms because it is interpreted in its boolean logical sense, not its natural language sense. See the subsection on "Selection Algebra" below.

namely something like (this command worked BEST for my case; it's all one line connect it where the backslashes ...lains about the '''codec''' part, then replace the word '''codec''' in the command line with '''vcodec'''.

Fortunately, the Python interpreter and the PyMOL command and selection languages make it possible to extend PyMOL safely and quickly * IPython integration (interactive shell): a robust alternative to the PyMOL command line?