[Chimera-users] generating a density map

Tom Goddard goddard at cgl.ucsf.edu
Tue Dec 9 15:43:14 PST 2008

Hi Jeff,

  The Chimera molmap command will make a map by placing Gaussians at a 
set of points (atoms or markers).  Its intended to simulate an EM map.


  All the points use the same standard deviation which is the same along 
all 3 axes.  But you could then change the voxel size of the resulting 
map (to say stretch z) using the Coordinates panel of the volume dialog 
or the volume command to get anisotropic Gaussians.


William Jeffrey Triffo wrote:
> hello,
> I remember seeing a pdb-to-density-map discussion at some point on this 
> mail list, maybe using something from the EMAN package (pdb2mrc or 
> something like that)?
> At any rate, a colleague recently asked me if I knew a way to generate a 
> density map from point-cloud data that he has. This sounds a lot like 
> the same question, except his data is anisotropic in z, so instead of 
> assuming an isotropic/spherical gaussian around point centers, he has 
> different sigmas for x/y and z.
> Does anyone have an algorithm he might be able to use to generate an MRC 
> map from this kind of data? He is wanting to do some volume 
> visualization, but to use Chimera he would need some sort of volume map 
> (such as MRC).
> thanks for any advice on this,
> -Jeff

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