[Chimera-users] Measuring Beta Barrels

[Elaine Meng]

Hi Danielle,
There is no direct measurement of this type in Chimera, but I will outline a few ideas. They are not particularly exact, but may be good enough for rough comparisons.  Also, some barrel structures have loops or other structures inside the barrel, so depending on your goal you may want to delete those parts first.

(A) Make a "volume" isosurface that fills the cavity, then slice it with a clipping plane and measure the surface area of the planar intersection.  I know of at least one web server that will calculate a volume within a cavity, 3V:  <http://3vee.molmovdb.org/>

The channel options might work but I usually just use the solvent one to get all the cavities and pockets.  Just as a test I opened 1gfl, deleted chain B and residues :52-90 which go through the middle of the barrel, saved that PDB, then uploaded it to 3V to do a solvent volume calculation.  I used the default parameters (think about whether you want to modify them for your own purposes) and medium resolution and in a minute or two it gave me a nice volume.  Opening the resulting mrc file in Chimera automatically starts Volume Viewer.  I moved the bar in Volume Viewer to adjust the isosurface level and then had a nice view of the cavity volume, figure attached. 

Then view the barrel end-on and use the SideView front clipping plane to slice to the level you want, then start Measure and Color Blobs (under Tools... Volume Data) and use Ctrl-button 3 (or whichever button specified on the dialog) on the sliced face to get area and approximate size reported.
<zhttp://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblobs.html>

(B) Just measure distances between pairs of atoms to get the diameter (or if more like an ellipse, major and minor axes).  Could view the barrel end-on and use the front clipping plane as a guide to help get atoms that are approximately coplanar.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>

(C) The Volume Tracer tool allows placing markers and then creating a surface from those points.  
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html>

It might be difficult to place markers with mouse-click where you want them, so to try this I'd probably just manually text-edit to create a marker file and use coordinates of some previously chosen set of approximately coplanar circumferential atoms from the PDB file.  Marker file format is described here, you would also need the markers to be linked in the proper order:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#markerfiles> 
I attached an example file, markers.cmm.
Then open the marker file, select the marker model in Chimera,  create surface (see Features... Surface in Volume Tracer menu). 
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#surfaces>
Then use Measure and Color Blobs as in (A) to get the surface area.

(D) The Axes/Planes/Centroids will calculate a best-fit plane for a selected set of atoms and report the radius.  However, this plane representation is always circular.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>

I am sure there are many other possibilities, both within and without Chimera. There are many web servers and other programs for cavity analysis.  Just a few (try web search if you want more details) are MolAxis, Caver, Hole ...

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 Jun 15, 2012, at 10:38 AM, Danielle L'Heureux wrote:

> Hi - 
> We are using Chimera to analyze fluorescent proteins, and we want to cluster and compare the barrels of each protein by examining a cross section of the FP beta barrel. Is there a way to measure the ellipsoid shape of a "slice" of a protein? Or is there a way to create an elliptical plane from which we can then calculate the area?
> Thank you,
>     Danielle L'Heureux

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