Hi Sarah, You can use the keyboard shortcut "bv" to create a new map that covers your PDB model. To enable keyboard shortcuts use Tools / General Controls / Keyboard Shortcuts and turn on "Enable keyboard shortcuts" in the dialog. Select the atoms of your PDB model. If you have more than one map open make sure the highlighted one in the volume dialog is the crystal map for the selected atoms. Then type the "bv" shortcut to create a new map covering the select atoms. This assumes that the starting map is a full unit cell. If you don't want to go to the trouble of enabling keyboard shortcuts, you can use the command "ac bv" which runs the shortcut (accelerator) bv. You can save the covering map with volume dialog File / Save Map As.... Tom Sarah Boyce wrote:

Hi Tom- I was told you might be the person to ask about the density map features in chimera. I'm trying to display crystallographic electron density maps and I've run into a problem aligning some of the maps to the protein model. When I load the map and model it looks as though the map is of the symmetry related molecule, but when viewed using Coot it automatically centers the map on the model. So far the only tool that I've found to do this is by hand alignment, which doesn't work at all for an atomic level model (or at least when I've tried it it is too much of a pain). Is there an automated tool in chimera that will automatically center the map on the model similar to the way Coot handles it?

Thanks, Sarah