[Chimera-users] Fwd: Does volume outline is bigger than actual volume?

Tom Goddard goddard at sonic.net
Tue Nov 21 11:44:12 PST 2017

Hi Michał,

  The values of a 3d image (volume) are considered to be intensities at a 3d grid of points.  Each of these points is at the center of a small cube called a voxel, the size of a voxel is part of the image file and is sometimes referred to as the grid plane spacing.  The outline box exactly includes all voxels in the grid.  So for instance if your data is 2 by 2 by 2 grid points with voxel size 1.2 Angstroms along each axis, then the outline box with be 2.4 Angstroms on a side.  The rendered graphics, either contour surface, or solid (volumetric) rendering only extends to the boundary grid points and does not cover boundary voxels.  So the surface or solid leaves half a voxel padding around the boundary relative to the outline box.  The reason for this is that surface and solid rendering uses linear interpolation of data values between grid points — since there is not grid point beyond the boundary it cannot interpolate beyond the center point of the edge voxels.  That would require extrapolating or making some assumption like the values are zero outside the grid, and Chimera does not do that.


> On Nov 21, 2017, at 8:40 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> From: Michał Kadlof 
>> Subject: Does volume outline is bigger than actual volume?
>> Date: November 21, 2017 at 6:00:17 AM PST
>> Hello, 
>> I need to understand precisely what Chimera do. Please look at the attached screen shoot. The arrows are anchored in point (0,0,0), and they are point in direction [(1,0,0),(0,1,0),(0,0,1)] red, yellow and blue respectively.
>> I set my volume to minimum (grey cube), I checked "Show outline box using color", and I noticed it does not cover the shape of my volume.
>> There are "margins" in the top, and the bottom visible in the image and much smaller on the sides.
>> Why they are there? What is its exact size? Where does volume actually begins in the (0,0,0), or slightly below that point?
>> --
>> ​best wishes,
>> Michał Kadlof <m.kadlof at cent.uw.edu.pl <mailto:m.kadlof at cent.uw.edu.pl>>
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