[Chimera-users] showing buried pocket
pett at cgl.ucsf.edu
Thu Apr 17 16:36:49 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.
> Have I explained that clearly enough???
If this is a standard PDB you can fetch the structure from the CASTp
database (File->Fetch By ID...) which will bring up an interface that
will allow you to browse the pockets of the structure, with only the
browsed pocket being surfaced.
If you have a non-standard PDB, you will need to identify some
residues near the pocket (let's say they were residues 15 to 19) and
then use a command like:
~surf :15-19 z>5
to hide surfaces further than 5 angstroms from those residues, which
should hide most of the "outside" surface. Then:
will hide the structure. If you don't know the pocket residues, you
might clip through the outside surface with the Side View clip planes
and then use the mouse-hovering popup balloons to identify some
If your pocket has a channel to the outside, you might want to get a
clean cut through the channel by using per-model clipping on the
surface and orienting the clip plane so that it cuts the channel.
The Per-Model Clipping tool is in the Depiction tools category.
I'd like to get Chimera to handle CASTp results for non-standard
PDBs, but haven't gotten to that yet.
UCSF Computer Graphics Lab
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