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.
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