[Chimera-users] Question about measuring volume in chimera

[Varun Kumar]

Thanks


On Tue, May 7, 2013 at 1:08 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Varun,
> Not exactly: Chimera can only measure the volume of an enclosed surface,
> such as a pocket that does not have openings to the outside.
>
> (A) If the binding pocket is completely enclosed by the molecular surface:
>
> You can use the Chimera tool "Measure and Color Blobs" (in menu under
> Tools... Surface/Binding Analysis) to measure the volume and surface area
> of that surface bubble:
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblobs.html
> >
>
> (B) If the binding pocket has one or more openings to the outside surface:
>
> Chimera cannot directly calculate the volume because it does not know
> where to draw the line (or plane) between pocket inside and outside.
>  However, it can show pocket volume and area measurements from the CASTp
> database. CASTp uses Delaunay triangulation and alpha shapes to find pocket
> boundaries.  If your structure is in the PDB, you can try fetching its
> CASTp data directly: use Chimera menu "File... Fetch by ID," choose CASTp,
> and enter the PDB ID code.  That also opens a copy of the structure, so it
> is best if you start with an "empty" Chimera.
>
> If your structure is not found in the CASTp database, you can go to the
> CASTp server and request a new calculation for your uploaded structure.  If
> you request the results to be e-mailed to you, the resulting files can also
> be displayed in Chimera.
>
> Please see this page for all the details on viewing CASTp information in
> Chimera:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html>
>
> CASTp server:
> <http://sts.bioengr.uic.edu/castp/calculation.php>
>
> I tried to manually position a clipping plane (with Tools… Depiction..
> Per-Model Clipping) to intersect with the molecular surface and thus
> "cover" an open pocket.  However, I couldn't think of a way to measure the
> volume enclosed by that intersection.  Also, it is geometrically impossible
> to do this for somewhat shallow pockets.
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
> On May 7, 2013, at 8:35 AM, Varun Kumar <vkumar1 at kent.edu> wrote:
>
> > Hi,
> >
> > Can we outline a particular area and measure volume in chimera?   I wish
> to measure specifically the purine binding site in the ATP binding pocket
> of Protein kinase C.
> >
> > Best regards
> >
> > --
> > Varun Kumar
> > International Graduate Student
> > School of Biomedical Sciences
> > Department of Biological Sciences
> > Kent State University, Kent, Ohio, U.S
>
>
>


-- 
Varun Kumar
International Graduate Student
School of Biomedical Sciences
Department of Biological Sciences
Kent State University, Kent, Ohio, U.S
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