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 chimera/share/VolumeData/mrc/mrc_format.py 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. Tom