[Chimera-users] Displaying and calculating protein surface enclosed pockets

Matthias Fellner mfellner at chemistry.otago.ac.nz
Thu Apr 30 20:34:38 PDT 2015

Good day

I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I always cite your citation for sure when I publish using your software.

Normally I get very far with your tutorials but this time I failed to achieve my goal and I wanted to write a direct question.

I have a protein with an active site pocket. I can display the surface of the protein and then I see the pocket inside but I am really interested in the enclosed surface = the active site pocket.

How can I display the "negative" (enclosed) surface area and possibly calculate its volume. Can this be done with the pdb file or is such an analysis only possible based on the electron density. I learned how to manipulate the density map in chimera, so if this is the only way I should also be able to do it if you explain the details.

If I get this done I wanted to ask if there is a way to ignore water molecules from the displaying of surfaces and later calculations or if I should simply work with a pdb which has the waters removed.

Thank you
Matthias Fellner
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