[Chimera-users] origin of volume data

Greg Pintilie pintilie at mit.edu
Thu Mar 27 13:57:28 PDT 2008

A question about data origin in densiy maps...

I open a map using the python script (in IDLE):
>>> import VolumeData
>>> gd = VolumeData.mrc.open ( "MRC map file" )[0]

looking at the origin of this map:
>>> gd.origin
(-135.679992676, -135.679992676, -135.679992676)

It is different than the origin reported if I open the same map file in
Volume Viewer; pasted from the Volume Viewer dialog:
-136.75 -136.75 -136.75

Why the difference? As to why I care, it's because if I open the map as in
the python script above and then subsequently use it to compute average
density values for certain structures, they are different than the average
density values reported in the 'Fit Model in Map' dialog. It would give me
more peace of mind if they matched...

Now to start speculating on why the difference, I've seen that, internally,
MRC maps define the origin in terms of a grid value, for example -64,-64,-64
in a 128x128x128 map. So the first value for the origin, as in the script
method above, is calculated as if the origin is at the _center_ of the first
grid point:

origin[0] = -64 * step + step/2

(where step is 2.13669279804), while the second value (showing up in Volume
Viewer) is simply calculated right on the grid point:

origin[0] = -64 * step

What's the right way to think about this? In the worst case, it's really a
pretty small offset so not a big deal.

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