[Chimera-users] occupancy calculation

[bala]

Hello,

1) I want to calculate the occupancy of water around few base pairs in a RNA duplex.  I had one query while i was going through the "calculate atomic occupancy" documentation.

"For example, cations or water hydrogens may tend to occupy space around a negatively charged solute group"

In the options give for this particular calculation, nowhere there is an option to select whether i am interested in WATER or ION occupany. How then chimera calculates the occupancy.

2)I presume that chimera calculates the occupany of say water as follows, if i select a residue, it puts the residue in a grid and calculated the density of water molecule in the grid points in frame. Is this the way it calculates the occupancy.

I am not getting how i should differentiate occupancy and density.


thanks,
Bala

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