Hi Bala, Elaine Meng answered these questions before I finished my email. I think my answers are the same, but I'll give them to you anyways. If the solvent map and reference PDB structure produced by Amber8 do not align when displayed in Chimera that is probably a problem with Amber or how you are using Amber. If they do not align I do not think you will be able to align them in Chimera. The one thing you could try is to use volume dialog menu entry Features / Origin and Scale. That will show the grid plane spacing (called "voxel size") and the origin that is being used for the map. You can try changing those values by hand. Press the Enter key after changing a value to have the display updated. Chimera can compute solvent occupancy from a trajectory using its MD Movie tool. See the "occupancy analysis" section of the Chimera documentation: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.ht... Perhaps this is an alternative way to do what you want. The threshold level in the Chimera volume dialog specifies what map value the contour surface is drawn at. The displayed surface goes through those points in space where the map has the specified value. What that means depends on what the values in your map mean. I don't know what the values in your solvent map computed by Amber8 mean. Here is the Chimera users list (found under the Contact Us link on the main Chimera web page): http://www.cgl.ucsf.edu/pipermail/chimera-users/index.html Tom