[Chimera-users] Inner Cavities

Mueller, Juergen-Joachim jjm at mdc-berlin.de
Fri Jun 17 02:53:24 PDT 2011

Dear helper,

I know the general pathway to get an inner cavity with CHIMERA 1.5.2
tools surface surfnet #0 MESH Apply
control click on mesh (all bubbles selected)
commandline:ac Sc
control click on bubble of interest (select only 1 bubble)
select invert (selected models) all wrong bubbles are selected
action surface hide

My problem is, there is no inner bubble detected in my molecule but there is one!
There were ligands which have been removed before.
What happens? Is there a probe sphere too large? Where can it set smaller?
Thank you for help,
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