[Chimera-users] Inner Cavities

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 17 10:01:22 PDT 2011

Dear Juergen,
I would use a regular molecular surface instead of the surfnet surface. Surfnet has parameters you can play with, but personally I find it more difficult to control the outcome than with the molecular surface.

If your structure is in the CASTp database, you could just fetch results including all the precalculated cavity volumes and surface areas, into Chimera.  Chimera uses the regular molecular surface to display the CASTp results, but also lists them in a convenient table.
For example, use File... Fetch by ID, enter a PDB ID in the CASTp fetch area -- I know 2gbp is in that database, but you could try your own PDB IDs of interest.  The advantage of the CASTp approach is that even if the pockets are not closed, it figures out boundaries between the pocket and the outside space and can report pocket volumes.


Or, if your structure isn't in CASTp and/or you just want to explore the bubbles yourself, you could use a similar process as you described, but with a molecular surface instead of a Surfnet surface.  For example:

open 2gbp
color white,s
surftransp 75

... then Ctrl-click to select the whole surface, then click the green magnifying glass at the bottom right of the Chimera window to open the Selection Inspector.  In that dialog, inspect "MSMS surface":
(a) change "one transparent layer" to false ... now you can see inside bubbles
(b) if you don't see the one you expect, you can also change "probe radius" in that dialog

Once you see there is a bubble of interest, you can use command "ac Sc" and continue as you said.  The molecular surface can also be shown as mesh, but I think it is easier to see the bubbles with transparency.

One problem is that the molecular surface calculation may fail numerically with certain sets of parameters.  In that case you could try different combinations of molecular surface probe radius and vertex density.


I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 17, 2011, at 2:53 AM, Mueller, Juergen-Joachim wrote:

> Dear helper,
> I know the general pathway to get an inner cavity with CHIMERA 1.5.2
> e.g.
> 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,
> Juergen

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