Hi Jason, Saving multiple maps in a single file is possible with a file format that is only used by Chimera. I don't recommend it. Maybe you are interested in adding one map to another. Chimera doesn't do that currently though I could add it. Chimera does allow you to recalculate a map at the grid points of a second map using interpolation, called "resampling". The resulting map can be saved and can be added point-wise to other maps having the same grid using other software (e.g. EMAN). To resample a volume use the "vop" command (volume operation) with the resample option, for example, volume #1 resample onGrid #0 calculates the map with model id 1 on the grid of map with id 0 and creates a new map. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html If your goal is just to save the fitting of one map into a second map then you can save the Chimera session. But if you want to be able to open those maps in another program and have them align you would need to do the above resampling so that both maps have the same grid and save the resulting map. Then other programs will show both maps with the desired alignment. Here are more details about the Chimera format the can handle multiple maps in one file. First, there are no commonly used file formats that I know of for x-ray or EM maps that hold multiple maps. Some formats of this sort are used in light microscopy for handling multi-wavelength images. There is a prototype file format called "Chimera map" based on HDF5 that can do keep many maps in one file, but only Chimera reads and writes this format. You write multiple maps to one cmap file with the "volume" command with "saveFormat cmap". The "append True" option allows you to append to an existing file. I don't recommend using this as it was written just to explore desirable capabilities for a new EM file format. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output Tom