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
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