PISA reports ASA/BSA on residue level as well. Internally, it keeps information on atomic level (including ASA/BSA "per atom"), but the atom-level output was never done. The reason is, I could never imagine that such level of description has any good meaning. "Surface area" is an abstraction for _macro_-objects, somehow applicable to macromolecules, but its physical meaning on atomic level is not very clear, apart from simplistic geometrical considerations. This has to do with the crossection of interactions, which is specific to the process in question. Surface atoms are much less static than residues, therefore their surface areas should fluctuate a lot more in the ensemble. I would therefore think that appealing to "surface areas" of individual atoms should be quite an overdoing. This is only to explain why atom-level output was not done in PISA.
Eugene. On Mon, Sep 28, 2009 at 11:48 AM, Eleanor Dodson <[email protected]>wrote: > Daniel Bonsor wrote: > >> I am trying to calculate the contact surface area of a loop. Using >> ArealMol >> I only get the overall contact surface area per residue. Is there any way >> to >> get it per atom or does anyone know of a program (online/software) which >> will perform this task. >> Thanks in advance >> >> >> Dan >> >> Daniel A. Bonsor, >> Boston Biomedical Research Institute, >> 64 Grove Street, >> Watertown, >> MA 02472 USA >> Tel: +1 617.658.7845 >> >> >> >> >> > Try PISA PDBePISA from the PDBe web site > Eleanor >
