[Chimera-users] occupancy calculation

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 9 10:03:01 PDT 2007

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,

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  
   select solvent
   select ions
Then you run the occupancy calculation. I hope this clears things up,

p.s. there are examples of occupancy calculation in Part 2 of the  
"Trajectory and Ensemble Analysis" tutorial

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

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