[Chimera-users] showing buried pocket
meng at cgl.ucsf.edu
Fri Apr 18 08:37:53 PDT 2008
> On Apr 17, 2008, at 8:59 AM, Gareth Young wrote:
> So I've been trying to make an 'inverted surface'. Basically I have
> a cavity inside a protein which is almost completely surrounded and
> so it is hard to illustrate it to others without removing parts of
> the protein (which I could of course do). Does Chimera have a
> function to mark the inside of a cavity with a surface, then
> allowing the user to remove the protein and just leave the surface
> so as to illustrate the size and shape of the cavity in relation to
> the protein.
Here is the man page on fetching CASTp data from Chimera:
Some of what I describe below is newish, so you would need to get a
daily build of Chimera to follow along:
Although not all protein PDB entries are in the CASTp database, you
can upload a structure to the CASTp server directly (not from Chimera):
At least the last time I tried it, if you choose the "E-mail only"
output option, one of the files it mails you contains only the atoms
that form each pocket. You could look at the text of that file, find
the pocket of interest, and then only specify those atoms in the
"surface" command in Chimera. (It wouldn't work to just open a file
with those atoms and surface them, because the surface would
completely enclose the atoms, not just the "real" surface side.)
This process is much more tedious than the direct fetch, however.
Even if you surface only the pocket atoms, there are other issues.
One problem is that Chimera only turns on/off surface patches per
atom, and sometimes the same atom has surface on one side that is
part of the pocket, but also surface on another side that is part of
some different pocket or the protein exterior; when you show the
surface for all "pocket atoms" there may be some extra bits.
Example: use the command "open castp:2gbp" and in the resulting
dialog, make sure the Surface option is turned on and click on the
second pocket in the list. It may take a few seconds to compute the
surface. That pocket is completely enclosed, but some of the same
atoms have additional surface. Extra bits can be clipped away to
some extent, but you are limited by the planarity of the clipping plane.
Another possibility in Chimera is to use the Surfnet tool. I find it
often makes too many small blobs and requires experimentation.
Example: open 2gbp, delete ligand (to make the pocket empty), choose
Tools... Surface/Binding Analysis... Surfnet - Selected Atoms. Enter
(I know residue 154 is next to the pocket and include other residues
within 5 angstroms), set the color if you want to, click Apply.
That gives one extra small blob. Actually I tried 8 angstroms first
and that gave several extra small blobs. You can close (delete) the
entire Surfnet results in the Model Panel (under Favorites). You can
Ctrl-click the Surfnet surface to select it. You still can't control
the different blobs independently until you split that surface,
however (after selecting the surface, use command "ac Sc"). Then you
can Ctrl-click an individual blob, open the Selection Inspector
(Actions... Inspect), and change the blob's color, type of display
(mesh/dot/filled) and lighting, and whether it is displayed at all -
thus you can hide the extra blobs.
In fact, several separate programs have been developed to show pocket
or tunnel surface or void volume:
Hole (can't find a current web page)
Hollow http://hollow.sourceforge.net/ (you may enjoy the Munch
painting in this page!)
I haven't had the activation energy to try any of these myself, and
unfortunately none have been specifically adapted to work with
Chimera (or vice versa). Caver has a Pymol plugin.
I hope this helps,
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
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