Hi Dhiraj, Ah, ok you have a map of the cavity created by voidoo. So you could use the "distance to surface" Chimera plugin I mentioned, make a small addition to the code to select the atoms close to the surface (rather than just print the distances). All in all it would be more work and give a slightly different results I think than the cavity surface residues listed by voidoo. Also this Chimera code is all in Python and is quite slow, so the distance to the surface calculation takes some seconds per atom for protein size surfaces, and that could take some time to calculate for thousands of atoms in your channel. If you wanted to try it nonetheless, you would add two lines of code to the "distance to surface" plugin, file SurfaceDistance/surfdist.py, line 32, just before the line for a, dmin, sxyz, side in dlist: put in two lines as follows: from chimera.selection import setCurrent setCurrent([a for a,dmin,sxyz,side in dlist if dmin <= 3.2]) You need the same indentation because that is important in Python. Tom