[Chimera-users] showing a cavity

Pu Qian p.qian at sheffield.ac.uk
Fri Oct 5 01:47:22 PDT 2012

Dear Dr. Meng,

Thank you very much for your email. I will try the ways you suggested and
let you know result.

Best regards


On 5 October 2012 04:26, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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)
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/clipping.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sop.html#cap>
> 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."
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblobs.html
> >
> 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
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
> 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):
> <http://3vee.molmovdb.org/>
> 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:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html>
> 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 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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