<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"><HTML DIR=ltr><HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1"></HEAD><BODY><DIV><FONT face='Arial' color=#000000 size=2><FONT face="Times New Roman">Hello,<BR><BR>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.<BR><BR>"For example, cations or water hydrogens may tend to
occupy space around a negatively charged solute group"<BR><BR>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.<BR><BR>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.<BR><BR>I am not getting how i should
differentiate occupancy and
density.<BR><BR><BR>thanks,<BR>Bala</FONT><BR></FONT></DIV></BODY></HTML>