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
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...> (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@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
Thanks On Tue, May 7, 2013 at 1:08 PM, Elaine Meng <meng@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...
(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@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
participants (2)
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Elaine Meng -
Varun Kumar