Hi Buz, Sorry to respond a little late, but if you are still tinkering with surface accessibility calculations, you can use the following web server that will calculate the "diffusion accessibility" of each atom in your input .pdb file:
http://nihserver.mbi.ucla.edu/diff_acc/ "Diffusion accessibility" is slightly different from "surface accessibility," so depending on what you're interested in this may not be exactly what you want. From the web server: "Diffusion accessibility gives a measure of surface accessibility that is longer range in nature than ordinary solvent accessibility. The idea of diffusion accessibility was introduced several years ago (Yeates, TO (1995) Algorithms for Evaluating the Long-range Accessibility of Protein Surfaces. J Mol Biol 249(4): 804-15). Diffusion accessibility is a measure of how easily or frequently a specific point on a surface would capture a hypothetical diffusing (or randomly-walking) probe that is captured upon its first encounter with any part of a surface. Naturally, parts of a surface that are solvent-exposed in the traditional sense but lie in a deep surface depression will capture the probe only rarely, since the probe will more often encounter another part of the surface first. The results of a diffusion accessibility calculation can be useful in quantitatively evaluating potential binding regions of a protein surface, and are particularly useful in visualization." The reason I still mention this is because diffusion accessibility vs. surface accessibility may be one way to answer your question of how to identify a surface residue vs. an interior residue. Also, the web server will output another .pdb file with the diffusion accessibility for each atom rewritten into the B-factor column. This is particularly useful for visualizing the "surfaceness" (as Ed put it) of each atom because you can open the output coordinates in PyMol and color atoms by B-factor which will give you a nice, colorful representation of the accessibility of the surface. Hope this is helpful, Mike ----- Original Message ----- From: "Buz Barstow" <b...@mac.com> To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, November 3, 2010 6:55:54 AM GMT -08:00 US/Canada Pacific Subject: Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues Dear All, Thanks for your suggestions! I ended up using the areaimol program in ccp4. My next question: Given a list of accessible surface area, is there a generally accepted value of ASA above which a residue classifies as a surface residue, while below this number it is an interior residue? Thanks! and all the best, --Buz On Nov 2, 2010, at 10:56 AM, Tim Gruene wrote: > Hello Buz, > > I do not know what you mean by 'linear map', but according to its manual, the > ccp4-program "surface" writes a list of accessible are per atom per residue, > which you could convert into the total fraction per residue with not too much > effort. > > Is this what you are looking for? > > Cheers, Tim > > On Tue, Nov 02, 2010 at 10:36:56AM -0400, Buz Barstow wrote: >> Dear All, >> >> I'm looking for a software program to produce, given a 3D atomic structure >> of a molecule, a linear map showing the surface accessibility of residues in >> a protein structure. >> >> Would any one know of a program that can produce this sort of map. >> >> Thanks! and all the best, >> >> --Buz > > -- > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > phone: +49 (0)551 39 22149 > > GPG Key ID = A46BEE1A > -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
