On 14/12/11 23:14, Jacob Keller wrote:
is there a convention for denoting/measuring pore sizes in protein structures? Maybe inter-atom distances minus van der Waals radii?
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.
