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" <j-kell...@fsm.northwestern.edu> To: CCP4BB@JISCMAIL.AC.UK 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 -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ******************************************* -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
