[Chimera-users] occupancy calculations

Eric Pettersen pett at cgl.ucsf.edu
Wed Oct 31 16:46:53 PDT 2012

Hi Ben,
	I just added an option to MD Movie to allow atomic radii to be factored in.  The two options (other than the previous behavior which is also available) is to increment all grid cells within the atomic radii uniformly, or to increment those closer to the atomic center more.  The latter is a very simple scheme in that the "outermost" cells are incremented by 1, the next layer by 2, the next by 3, etc. with the center cell getting the highest increment.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Oct 31, 2012, at 9:49 AM, Tom Goddard wrote:

> 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 sphere.
>    Tom
>> 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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