[Chimera-users] occupancy calculations

Tom Goddard goddard at sonic.net
Wed Oct 31 09:49:50 PDT 2012

Hi Ben,

   The MD occupancy map can only record the center positions of atoms.  
After it is calculated you can use Gaussian filtering, for example,

     vop gaussian #1 sdev 6.5

to convolve the occupancy map with a Gaussian.  Equivalently you could 
use the Volume Filter dialog (menu Tools / Volume Data).  Of course both 
of these are not quite the same as putting a Gaussian at the atom center 
positions and then accumulating because the above procedure first 
discretizes the center positions by recording them in the occupancy grid 
before we apply the Gaussian.  But the difference will be small if the 
grid size is fine.  We don't currently offer any other kernels such as a 


> Hi list,
>    I am using the MD->occupancy tool to produce occupancy densities of a very coarse grained model (I have a few spheres, with big radii : approximatively 10 spheres with 10A radius each). My problem is that the density is computed only for the center of each sphere, which tells me where the center stands. To have a better feeling of the space occupied by each sphere I'd rather like a density computed for the whole sphere (updating each cell of the grid by either incrementing if the cell is covered by the sphere, or why not with any type of kernel centered on the sphere and depending on the sphere's radius.).
>    Can I do that with Chimera ? And if so, How ?
>      thanks
>       --Ben

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