not sure if this has made it yet into the open source version, but to quote the incentive version documentation “Beginning with incentive PyMOL 1.6, arbitrary object level and atom level properties are supported. Now, for each object and each atom you can possibly have an arbitrary dictionary associated with each.” So if you are a subscriber you could make use of that feature, which could be more powerful than relying either on the B-factor or Occupancy fields.
From: Chen Zhao [mailto:firstname.lastname@example.org]
Sent: Friday, August 29, 2014 12:25 PM
Subject: [PyMOL] Other coloring strategies based on user-provided properties
I am thinking whether it is possible to color a molecule by a specific property residue-wise or atom-wise like generally be done on B-factor? This property could be provided as numbers in a column. An obvious way might just be to change the B-factor column to the user-provided column and "color by B-factor". But I am wondering whether there are some direct ways of doing this.