Hi All, Amongst my colleagues (to whom I constantly evangelize Chimera) there is often an issue opening pdb and map files together. Specifically, sometimes the maps and pdb coordinates are not superimposed (often drastically). I have been able to reproduce the issue so let me explain what works and what doesn't. What works: If you take a pdb file and an mtz into Phaser (from the ccp4 suite) then refmac for rigid body refinement and convert the output mtz to a map using mapman it works. The pdb and map superimpose perfectly. What doesn't work: If you take a pdb file (of known correct solution but not transformed to the correct coordinates) and throw it into refmac (ccp4) and do some rigid body refinement and then convert the resulting mtz into a ccp4 map, the map is perfectly good (the statistics are identical to using the phaser placed model), but when opened in Chimera they do not superimpose. Both of the methods above appear valid as far as structure determination (R and Rfree are identical, etc) and I know coot will align the model and map and I believe pymol will too, though I don't use pymol personally so I cannot vouch for that. Is the correct transformation information hidden in a file somewhere so that Chimera can align the two files automatically. Often people skip the phaser step and drop the model right into refinement and then manually aligning in Chimera becomes difficult. Best, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405