[Chimera-users] showing a cavity

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 4 20:26:23 PDT 2012

Hi Dr. Pu Qian,
There are a few possibilities:

(A) in Chimera, if the complex is a single model (or if separate, you can combine into a single model using "copy/combine" in the Model Panel), you may be able to show this cavity by displaying a molecular surface for the whole complex and then using global or per-model clipping to slice the surface.  You could try showing the clipped surface with capping on or off to see which you like better (e.g. command: sop cap off)
One possible problem, however, is that molecular surface calculation may be more prone to failure on large complexes.  Also, if you wanted to not only show the cavity but also to measure the volume using Chimera, the cavity must be completely enclosed with no openings to the outside.  To measure the volume of an enclosed cavity, use Side View to clip so that you will be able to click the on the cavity surface, then use "Measure and Color Blobs."

If the surface calculation fails...

(B) the molecular surface can be roughly approximated by an isosurface of a density map simulated from the structure.  For example, command: molmap protein 5
The tricky part here would be deciding what isosurface level gives a reasonable approximation to the molecular surface.  Again, the cavity would need to be completely enclosed if you want to measure its volume in Chimera.  The measurement would be done as described in (A).

The next two approaches allow both visualization and measuring volume even if the cavity has openings to the outside.  They also involve use of web servers outside of Chimera.  I haven't tried these web servers on very large structure.  Also, you may not want to use web servers on your private data.

(C) create a map of the empty space with the web server 3V: Voss Volume Voxelator (I use the "Solvent Extraction" option to find cavities):
You can open the map file in Chimera, then measure the isosurface-enclosed volume as described in (A).

(D) CASTp is a database with pocket surface areas and volumes for many (most?) PDB entries.  You can fetch CASTp data directly into Chimera, for example by choosing menu entry "File... Fetch by ID" and then indicating CASTp database and giving a PDB ID code.  If your structure is not in the PDB, or if it is in the PDB but not in the CASTp database, you can go to the CASTp web site and upload your structure for a calculation, and it can send you the results back by e-mail.  Then you can open the results in Chimera.  Details on using CASTp data in Chimera:

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 Oct 3, 2012, at 2:29 PM, Pu Qian wrote:

> Hi,
> I'm working on a big protein complex with MW ~500 kD. It contains a cave inside of the protein. Now I would like to high light this cave so that I can show the room that is big enough for a quinone molecule to move. Question is: is there a function in Chimera which allows users to produce such cave inside of the protein based on PDB file of the protein. If is, where can I find it and how to use it. It would be a great appreciated if anyone here could give me advices. Thanks.
> Best regards
> Dr. Pu Qian
> Department of Molecular Biology
> The University of Sheffield
> Sheffield, S10 2TN
> UK

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