Dear Tim, Re your last paragraph on how much trust one can place in such calculations I draw your attention to our recent study:-
S.J. Fisher, J. Wilkinson, R.H. Henchman and J.R. Helliwell “An evaluation review of the prediction of protonation states in proteins versus crystallographic experiment “Crystallography Reviews Vol. 15, No. 4, October–December 2009, 231–259. All best wishes, John Prof John R Helliwell DSc On Thu, Mar 25, 2010 at 4:43 PM, Tim Gruene <[email protected]> wrote: > Hello Rebecca, > > this is merely a guess, but I think, it should work. > > As you calculate the electrostatic surface potential in pymol, it uses > apbs. > apbs, if I remember correctly creates an intermediate PDB-file where the > B-factor column is replaced with the partial charge of that atom. > > So if you can get hold of that file you can use a text editor to cut out > the > helices of interest into separate files and use shell commands to sum up > the > B-factor columns. > > The following (all in one line, in case any mail program splits the line) > adds > up the B-values in the PDB-file: > > grep "^ATOM" helix.pdb|cut -c61-66|awk '{pcharge += $1}END{print pcharge}' > > Having said that I would be curious to hear what the community has to say > about > how trustful and meaningful such calculations actually are, because I have > always wondered about this since I looked at my first GRASP surface. > > Tim > > > > > On Thu, Mar 25, 2010 at 11:03:29AM -0400, Page, Rebecca wrote: > > Dear CPP4 community, > > > > > > > > I am in search of a program that will calculate the net charge of an > > electrostatic surface formed by individual secondary structural elements > > (versus the entire protein) of a structure: for example, the net charge > > of the electrostatic surface of helices 2 and 3 versus, say, helices 3 > > and 4 of the same protein. > > > > > > > > > > > > Thanks in advance, > > > > > > > > Rebecca > > > > > > > > > > > > -- > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (GNU/Linux) > > iD8DBQFLq4SjUxlJ7aRr7hoRAkJwAKCe/Lq7XwuFoRwAIs76Xn82AYsqsQCgrpKA > dkkgJtdxdH9L2P2RGdH87JQ= > =qEsR > -----END PGP SIGNATURE----- > > -- Professor John R Helliwell DSc
