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2007.06.07 -- This application has been archived. Local users, see a CSB staff member for help if you need to run this program in the Core.


pretty picture of HOLE cavity through the channel form of gramicidin

HOLE is a molecular graphics program for visualization and analysis of the holes through atomic models of ion channels. It was written by Oliver Smart.

The User Manual is available locally on-line.

The HOLE progam was bequeathed to the Sansom group at the University of Oxford, which apparently no longer officially supports it.

Other, more up-to-date programs for channel analysis include Caver and Mole.

To get started, type:

setup hole (or source /srv/local/setup/hole.set)

You will then have the following executables in your path:

HOLE requires a command file as input. A typical first command would be:

hole < hole.inp > hole.out

See the manual for syntax to run other programs.

Note: If you publish any results from the use of this program please reference the following:

O.S. Smart, J.M. Goodfellow and B.A. Wallace (1993) The Pore Dimensions of Gramicidin A Biophysical Journal 65:2455-2460.

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Last Modified: Friday, 18-Jul-2014 09:35:20 EDT by P. Fleming