From: Aaron Oakley (
Date: Thu Oct 27 2011 - 01:30:23 CDT


I am trying to reproduce results reported in Cohen et al (2006) "Imaging the migration pathways for O-2, CO, NO, and Xe inside myoglobin"

Specifically, the result for Experimental PMFs of Xe calculated from PDB 1J52 using the relationship

PMF = -kB T ln((Xe occupancy) / 1 ^3/ P(Xe) / kB T)

Its not clear what is being done here.