Friday, 13 January 2012

Pore Dimension Convention

From: Jacob Keller


Dear Crystallographers,

is there a convention for denoting/measuring pore sizes in protein
structures? Maybe inter-atom distances minus van der Waals radii?

JPK

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From: Michael Thompson


Hi Jacob,

There are a number of programs that can calculate the radius of a pore. The one that comes to mind is called HOLE, and it can make a nice plot of the y-coordinate along the pore vs. pore radius. I don't recall exactly how this calculation is done, I think it is somehow related to the SASA (some sort of spherical probe type of thing), but I'm sure you can have a look at the documentation for more details.

A quick search also shows that there are apparently a number of tools out there that will do similar analyses. See this web page for a summary:

http://www.caver.cz/index.php?sid=133

Good luck,

Mike

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From: Paul Emsley

AFAIK, the standard method is HOLE (Smart, Goodfellow, Wallace, 1993 (for example)).

The method has been implemented in Coot using energy-lib.cif from the Refmac dictionary for the atom-type radii and is available (in 0.7-pre) by using the `hole' function.

http://lmb.bioch.ox.ac.uk/coot/doc/coot/hole.html#hole

(it's not on the caver page, which is why I mention it here).

Paul.

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From: Paul Emsley

Replying to my own post :-( ...

I forgot to mention that I wrote a GUI for it:

http://lmb.bioch.ox.ac.uk/coot/extras/test-hole.scm

Screeny here:

http://lmb.bioch.ox.ac.uk/coot/screenshots/Screenshot-Coot-hole.png


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