[chimera-dev] Origins in CCP4 and MRC maps

[Tom Goddard]

Hi Bernard,

  The Chimera origin reported in the Volume Viewer dialog is not the 
array index of physical origin.  It is the physical coordinate of array 
index 0,0,0.  So it is the inverse of how you are interpreting it.  
We've been using this definition since about 2000, before your 2006 
paper on conventions for EM maps.  With this understanding your example 
of a 100^3 map with physical origin at array index (50,50,50) and 2 
angstroms/voxel the index (0,0,0) physical coordinate is 
(-100,-100,-100) which you say Chimera reports for a CCP4 map.

  Chimera uses the xorigin, yorigin, zorigin header values (words 50-52) 
in MRC2000 format instead of the nxstart, nystart, nzstart header values 
(words 5-7).  You probably have (50,50,50) in the xyz origin fields while
Chimera expects (-100,-100,-100) in those fields.  The MRC documentation

    http://www2.mrc-lmb.cam.ac.uk/image2000.html

unfortunately does not describe the meaning of those origin fields, 
though I suspect your interpretation is correct as it agrees with 
nxstart,nystart,nzstart definition and would just provide floating point 
equivalents of those integer values.  Perhaps there is better MRC 
documentation defining xorigin,yorigin, zorigin.  Chimera writes MRC2000 
files and fills the origin fields with the physical coordinate of index 
(0,0,0).

  These different interpretations of the meaning of the origin fields 
are a big problem.  How are the xorigin,yorigin,zorigin fields in 
MRC2000 actually being used?  I know Chimera and EMAN both interpret it 
as a physical coordinate of array index (0,0,0).  From your comments I 
assume BSOFT interpets it as the array index of the physical coordinate 
origin.  What other software is using these fields and how do they 
interpret it?

  It would be a big problem to change the origin definition in Chimera 
because users have written many MRC2000 files using Chimera that would 
no longer be positioned correctly if the meaning of the origin fields is 
changed.  Chimera does not write information in the MRC labels header 
fields indicating which version of Chimera wrote the file.  That was a 
mistake.  So there is no way of telling which interpretation should be 
used for a Chimera-written MRC file.  EMAN currently writes a label line 
saying EMAN and the date and time the file was written.

    Tom