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
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