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
----- Original Message -----
From: "Jacob Keller" <[log in to unmask]>
To: [log in to unmask]
Sent: Wednesday, December 14, 2011 3:14:33 PM GMT -08:00 US/Canada Pacific
Subject: [ccp4bb] Pore Dimension Convention
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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*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [log in to unmask]
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Michael C. Thompson
Graduate Student
Biochemistry & Molecular Biology Division
Department of Chemistry & Biochemistry
University of California, Los Angeles
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