Hi Walter, With the help of your example CCP4 map I found that the problem was a heuristic used by the Chimera CCP4/MRC file reader to determine whether the (ncstart,nrstart,nsstart) header values are valid or appear to be uninitialized. If it found any n*start value to have absolute value larger than the original data size (mx,my,mz header parameters) then it considered the n*start position values out-of-range and probably uninitialized and used n*start values of (0,0,0). That messed up the position of the map you sent. I've changed this heuristic so that the n*start values only need to be less than 10 times the maximum data dimension to be considered valid. It would be nice to drop this heuristic altogether. Unfortunately some map files have uninitialized values that cause the map to be placed in deep space. The fixed Chimera code will be in the next snapshot (should be on the web on Friday from our automatic builds). If you wish to change your current Chimera code you can edit chimera/share/VolumeData/mrc/mrc_format.py replacing lines starting at line 87: if (nxs >= -mx and nxs < mx and nys >= -my and nys < my and nzs >= -mz and nzs < mz): from VolumeData.griddata import scale_and_skew self.data_origin = scale_and_skew((nxs,nys,nzs), self.data_step, self.cell_angles) else: self.data_origin = (0., 0., 0.) with limit = 10*max(max(mx,my,mz), max(self.data_size)) if [s for s in (nxs,nys,nzs) if abs(s) > limit]: self.data_origin = (0., 0., 0.) else: from VolumeData.griddata import scale_and_skew self.data_origin = scale_and_skew((nxs,nys,nzs), self.data_step, self.cell_angles) Make sure to keep the indentation as shown since that is important in Python. The above change is for Chimera 1.2422. Thanks for reporting the problem. Tom