Hi Dhiraj, You can select just the atoms in a map with some Chimera black magic. There is a keyboard shortcut "oa" that restricts the currently selected set of atoms to those that are above the threshold level of the volume data set shown in the volume dialog. If you start by selecting all atoms (menu Select / Select All or shortcut "sa") then use "oa" then you have the atoms outside the map selected, then invert the selection (menu Select / Invert or shortcut "is"). These Chimera shortcuts need to be enabled using menu entry Tools / General Controls / Accelerators On, and then you can type the two letter key sequences into the main Chimera window. Here's a list of other shortcuts. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.... Tom