We have an issue with disparity of the interpretation of CCP4 and MRC
density maps in Chimera. The CCP4 and MRC file formats are very close
in specification, and in particular the definition of the origin is
the same. However, when I open both formats of a density map in
Chimera, the origins given in the Volume Viewer do not agree and the
maps are located in different places.
The first issue is how the origin is specified. In the 3DEM
community, we proposed that the origin is defined as the location of
the physical coordinate origin within the framework of the map,
expressed in voxel dimensions. In Chimera (build 2422), the origin
for the MRC format is consistent with this definition while for the
CCP4 format it is not.
Example: I have a map with dimensions 100x100x100, an origin at
50x50x50 and sampling of 2 angstroms/voxel. In both the CCP4 and MRC
versions the relevant fields are: nxstart = -50, nystart = -50,
nzstart = -50. The origin as defined for 3DEM is thus the negative of
these fields. In Chimera, the origin is given as {50,50,50} for the
MRC format file, while for the CCP4 format file it is {-100,-100,-100}.
Suggestion: The origin given in the Volume Viewer for the example
should be either {50,50,50} specified as voxel units, or
{100,100,100} specified in angstroms, for both file formats.
Identical maps in the two formats should be superimposable when the
origin specifications are the same.
Bernard Heymann, Research Fellow
Rm 1515, 50 South Dr., MSC 8025, NIAMS, NIH
Bethesda MD 20892-8025
Tel. 301-451-8241, Fax. 301-480-7629
