This was a very helpful answer. If anyone would like to see equivalent c code, I'd be happy to post it.

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From Chris:


hi Josh-

I'm no programmer but I used this to pipe some output to pymol from perl:

$pid=open(PYMOL,"| $pymol_path -qpxif 0");

where $pymol_path was the path to the executable, this opens pymol in a viewer only mode.
one of those options allows pymol to listen to STDIN for input.

also perl needs:

PYMOL->autoflush(1);


HTH
Chris

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