Hi Albion, Elaine's suggestion to use the "Save relative to model" option when saving coordinates of PDB models fit into maps is the right solution. Here are a few more details about coordinates in Chimera. If you open a PDB model in Chimera its atoms are positioned at Chimera (x,y,z) coordinates just as they are specified in the file. When you rotate the model the atoms are now at different positions in Chimera coordinates. If you use File / Save PDB... without the "save relative to" option you will see that the coordinates in the new file are different from the original PDB file -- the file contains positions for the rotated molecule. If you open a PDB file and a density map, rotate both together, save the PDB file, then restart Chimera and open the original density map and the saved PDB file you'll see they no longer have the same relative position. The problem is that you saved the rotated PDB model but you are using the original (unrotated) density map. There is no option to save the rotated density map, and you don't really need that. Saving a rotated map would require resampling it at new grid positions because none of the map formats include an option for specifying a rotation in the header. You don't want to resample because it reduces the quality of your map. Instead you use the "save relative to" option when saving the PDB file to say to use coordinates relative to the orignal density map position, when it was first opened in Chimera. Effectively Chimera applies a rotation and translation to the PDB coordinates that places your density map back in its original position before saving the PDB atom coordinates. There is a bit more complexity to this. Chimera remembers the original PDB atom coordinates and the current rotation and translation which positions the PDB model from all your cumulative mouse or command rotations and translations. If you start Chimera and open a density map it appears in a standard orientation, x-axis horizontal, y-axis vertical, and z-axis pointing out of the screen. If instead you start Chimera, open a PDB model, rotate it, now open the same density map, it does not appear in the standard orientation! Instead it applies the rotation of the PDB model to the density map. This is a good behaviour. It means no matter how you rotate and move your PDB model before opening the density map, you end up with the PDB model and density map having the same relative placement as if you hadn't moved the PDB model at all before opening the density map. But it can get confusing. If you first open two PDB models, the move one of them with the other fixed (ie. deactivated), then open the density map, which PDB model does the density map align with? The two models now have different rotation/translations relative to their original file coordinates. The answer is that the density map gets the rotation/translation of the PDB file with the lower id number (shown in Model Panel). That might not be what you want. Model Panel has a "Transform As..." button that allows you to position the density map using the same rotation/translation as the other PDB model if that is what you want. Tom