VMD-L Mailing List

From: Filip Persson (filip.persson_at_gmail.com)
Date: Tue Sep 06 2011 - 03:08:20 CDT

Hello,
I am trying to define a cavity in a protein using the atom selection command
in VMD. I tried using

*water and within 3 of (residue X and residue Y)*

in the 'selected atoms-field' in the graphical representations window, but
nothing happens. Changing the distance does not help, so obviously I must be
doing something wrong here. Is it possible to define cavities in a way
similar to the command above, or should I use any other type of selection
command?

Thanks!

Best,
Filip