Hi Bala, There are several possibilities, but one easy thing is to use "Presets... Interactive 3 (hydrophobicity surface)" in the Chimera menu. This will display a molecular surface and color it by amino acid hydrophobicity (Kyte-Doolittle scale) from dodger blue at the most polar end, to white, to orange for the most hydrophobic. You can then visually inspect the surface for orange-ish pockets. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets A figure showing a hydrophobic pocket is included in the new "Structure Analysis and Comparison" tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html#surfaces You can use Render by Attribute to map different coloring schemes to Kyte-Doolittle hydrophobicity, as described in that tutorial. You can also read in different hydrophobicity scales as described here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html That covers the "what is hydrophobic?" part of the question. As for "what is a pocket?", you may wish to simply use visual inspection, as described above. Another approach is to use the CASTp database of pockets - very useful, but it does not include everything in the PDB. You can open a structure and its CASTp pocket data in Chimera using "File... Fetch by ID" or the command "open", for example: open castp:2gbp or open castp:4enl Just use the PDB ID of your structure. However, you may get a message saying your structure is not in that database. Here is the documentation on viewing CASTp data in Chimera: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html