[Chimera-users] Problems with binding site representation

[Elaine Meng]

Hi Vigneshwari,
The CASTp approach is great in that it automatically figures out for you where the pocket boundaries are (where the pocket ends and the outside begins), and provides volume and other measurements.  CASTp works with apo structures as well as liganded.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/castp.html>
<http://sts-fw.bioengr.uic.edu/castp/calculation.php>

Another tool that can be used with Chimera is the Voss Volume Voxelator (3V) web server, which will create "density"-type maps of the pockets and tunnels in a structure.   In Chimera, you can open the resulting map, adjust the isosurface level as desired in Volume Viewer, then measure the volume enclosed in the isosurface with the "Measure and Color Blobs" tool (in menu under Tools… Volume Data).
<http://3vee.molmovdb.org/>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblobs.html>

These do not display different inside and outside colors, but they use other ways to locate the pocket boundaries.  The complicated procedure in Chimera to generate the pockets with different inside and outside coloring is because we currently don't have 2-sided coloring on a single surface.   The map from 3V could be shown with two different isosurfaces slightly offset from each other in two differen colors, but I don't know how useful that would be.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>

You may need to use a different program if none of the above suffice.
Best,
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 Nov 11, 2013, at 11:14 PM, vigneshwari subramanian <vignesh.bioinfo at gmail.com> wrote:

> Hi Elaine,
> Thanks for your email.
> 
> Our aim is to show the differences in the volume of binding cavities when an agonist and antagonist binds. We also want to show the ligand free state of the cavity. The reason for having 2 different colors is to clearly see if the volume marks the inner or outer surface of the cavity.
> 
> Since this doesn't work very well, I thought I could solvate the cavity and display that surface. I am not sure if there better ways to represent the volumes of binding cavities.
> 
> regards,
> vigneshwari
>