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