[Chimera-users] Map Oddities

Thomas Goddard goddard at cgl.ucsf.edu
Fri Sep 22 16:06:48 PDT 2006

Hi Albion,

  An origin of (-224,-224,-224) does not seem consistent with the MAPMAN
header output you sent.  From that I suspect that you have an MRC 2000
file with xorigin, yorigin, and zorigin set and MAPMAN does not display
those header values.

  Here are two approaches to see the MRC header values.  You can add
a few lines to


to print all the header values that Chimera reads when the MRC map is opened.
After the lines

    v = self.read_header_values(file, file_size)
    self.check_header_values(v, file_size, file)
    self.header = v             # For dumpmrc.py standalone program.

add the additional lines:

    for key, value in sorted(v.items()):
      print key, value

Then restart Chimera and open the map and use menu entry Favorites / Reply Log
to see the printed header value.  If you see a "zorigin" value then you
have an MRC 2000 map.  My guess is you have it and its value is -224.

  The scale_and_skew() call you noted in mrc_format.py just multiplies
the integer origin by the voxel size and applies a skewing transformation
if the cell angles are not 90 degrees.  (They are 90 for your map.)

  The alternate approach is to use unix utility "od" (on Linux or Mac)
to print the binary header as ints or floats depending on the values in
the header you are interested in.


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