Hi Spyros,

> Creating selections the default way places pixel-size pink dots on
> the structure, so I was wondering if there is some way to control
> this for more complex visualization tasks?

set active_selections, off
set auto_show_selections, off

both seem to hide the pixels, but I'm not sure which one is the better 
to use. To find such settings, I can recommend 'grepset' from the 
PyMOLWiki: http://pymolwiki.org/index.php/Grepset

> Is there a way to color-code my selections, and visualize them
> simultaneously on the structure to see if there is any overlap?

See Tsjerk's reply.

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology

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