[Chimera-users] Origin question with maps

Tom Goddard goddard at cgl.ucsf.edu
Fri Jun 29 18:17:01 PDT 2007

Hi Eduardo,

  The MRC and CCP4 map file formats are almost identical.  There is a 
difference in how the origin is specified though.  In MRC 2000 format 
some of the reserved extra space in the standard CCP4 header is used for 
xorigin, yorigin, and zorigin floating point values.  The standard CCP4 
format does not have these fields and the origin is instead determined 
using integer ncstart, nrstart, nsstart header values.  These *integer* 
origin values are only adequate  for subvolumes of crystallographic 
density maps.  When you say that the CCP4 map does not align correctly 
does Chimera report your 1.mrc map origin as (0,0,0) instead of the 
desired (10,0,0)?  If that is the case then I believe the problem is 
with the code that wrote the map.  It did not set the ncstart, nrstart, 
nsstart parameters to specify a (10,0,0) origin (and it will be 
impossible in CCP4 format unless the grid plane spacing evenly divides 
10 because the origin header values must be integers).


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