Hi Bala, It counts the times the atom(s) appear in the 3D grid cells over the specified trajectory frames. It is not average density, but the total count in each cell over multiple frames, and the number is not divided by the volume of the cell. Typically to get a nice map at the end, you would use a small grid spacing so that there would not be more than one water or ion (or whatever atoms you choose, see below) in a given grid cell in a given frame. As described in the documentation, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ movie.html#occupancy there are two separate selection steps: (1) select the atoms to hold steady, then choose "Actions... Hold selection steady" from the MD Movie menu. This step is optional, for example, your trajectory might already be processed to hold certain atoms in place. (2) select the atoms for which occupancy (density, whatever) should be computed. This is where you would select solvent, ions, whatever. There are many ways to select: Select menu, picking from screen and arrow keys, or commands, for example: select solvent select ions Then you run the occupancy calculation. I hope this clears things up, Elaine p.s. there are examples of occupancy calculation in Part 2 of the "Trajectory and Ensemble Analysis" tutorial http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembles2.html#part2 On Jul 9, 2007, at 6:50 AM, bala wrote:

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