Bert; I have found the online gui 3V to be very useful in calculating channel dimensions. It outputs the volume and surface area of the pore, along with a surface representation that can be visualized in Chimera or PyMOL. You can either specify a specific pore or search for pores within a given size. There is other functionality available on the website for solvent volumes, etc.
http://3vee.molmovdb.org/ Regina ________________________________ From: "Van Den Berg, Bert" <lambertus.vandenb...@umassmed.edu> To: CCP4BB@JISCMAIL.AC.UK Sent: Wed, March 23, 2011 9:02:19 AM Subject: [ccp4bb] (off-topic) Measurement of channel pore dimensions Hello all, Does anyone know how to get values for pore sizes of membrane channels? I’m not interested in A x B angstrom values measured between atom centers and assuming a regular pore shape, but a “real-life” value of either surface area at the narrowest point or the volume of a block centered on the narrowest point of the pore. Thanks, Bert
