[Chimera-users] Problems with binding site representation

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 11 09:47:43 PST 2013

Hi Vigneshwari,
I don't know what you mean by "parameters" ... you probably don't want to mess with atomic or probe radii, for example.  What matters is how you split the atoms into two sets (i.e. which atoms you used as the ligand) and you didn't say what you did.  In this structure, you might use just RET, or you might also include part of Lys-296, to which it is covalently bound.

As mentioned earlier, the main limitation of the "measure contactArea" approach is that it requires two sets of atoms to define two surfaces, and thus does not apply to apo structures.

Keep in mind that some pockets really are enclosed, so it is not necessarily wrong that you don't see an opening to the outside.

I don't know if your goal is to just show a pocket surface or whether you really needed it to be different colors on the inside and outside.  If you don't care about the two colors, you don't need to use "measure" and it is MUCH simpler.  You can show any surface patches you want, simply by specifying which atoms' surfaces to display.  The hardest part is figuring out which atoms are lining the pocket.  It is easier when there is a ligand, because then you can use distance from ligand, as in this tutorial:

If you just want to display pocket surfaces for both apo and complex structures, I recommend taking a look at the CASTp interface in Chimera.  CASTp figures out which atoms line each pocket and also gives several kinds of information like pocket volume and number of openings. If your structure is already in the CASTp database, you can just use File... Fetch by ID in the menu and fetch if from there.  If it is not in that database, you can upload your structure to their webserver, get the results by email, and then load them into Chimera, which has a nice dialog for looking through all the different pockets.  Details here:

I hope this helps,
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 5:48 AM, vigneshwari subramanian wrote:

> Hi Elaine,
> Sorry to bother you again. 
> I tried to generate a similar figure for the PDB id: 1U19. I am interested in showing the surface around the ligand Retinal which is covalently bound to rhodopsin.
> The surface shown here looks a bit weird. Kindly check the attachment. Only part of the surface around the ligand is shown. Moreover the cavity remains closed. 
> I don't know how to adjust the parameters. I tried many options. But I couldn't extend the contact area so that it covers the whole ligand.
> Are there any options to do the same for apo structures?
> Thanks,
> vigneshwari

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