The Chimera molmap command creates a density map for a molecule using a grid that has its 3 axes aligned with the x, y, and z axes of the molecular data (atom coordinates) with padding 3 times the requested map resolution. This is described in the molmap documentation

The origin of the grid equals the x,y,z coordinates of the grid point at grid index 0,0,0. That origin position (floating point values) is saved in an MRC 2000 file in the xorigin, yorigin, zorigin header fields.

It cannot be saved in the nxstart,nystart,nzstart header fields since those are integer values and can't accomodate the exact floating point origin. Here's the Chimera Python source code that reads MRC files if you want more details of how that is handled.

On Jul 8, 2013, at 1:08 PM, Catalin Buiu wrote:

Hello all,

I have the following problem: when I use molmap to generate
a map from an atomic structure, the result is fine: both align.
When I use another (Matlab) program to generate the map, the two,
when opened in Chimera do not align anymore.
My question is how molmap generates an origin index such that
both the map and the structure do align and how Chimera reads (and converts)
the xyz origin data from the MRC file?

Thank you.

Catalin Buiu
University of Bucharest, Romania
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