[Chimera-users] Using Chimera to measure voxel densities

Tom Goddard goddard at sonic.net
Fri Jan 30 14:43:32 PST 2015


Hi Alex,

  You could get the interpolated density each atom position with the Values at Atom Positions dialog (menu Tools / Volume Data).  Usually this is used to color the atoms based on density value, but the values can be written out with the Render by Attribute dialog menu File / Save Attributes.

  It is not easy to see the positions of nearby grid points and those grid points can’t be selected. But if you really want to get at those values you might just display your map as a mesh and adjust the contour level by hand until you see the surface intersects a grid point (the contour lines in mesh mode lie in the grid planes so you may be able to visually see when the surface hits a grid point).

	Tom


> On Jan 30, 2015, at 1:33 PM, Noble, Alex <ajn10d at fsu.edu> wrote:
> 
> Hi all,
> 
> I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera?
> 
> Best,
> -Alex Noble
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