How about using the APBS plugin?
http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol

The plugin that is shipped with Pymol as standard
http://www.pymolwiki.org/index.php/APBS

The same plugin, but in the Pymol-script-repo
Here the plugin is setup to find the included (psize.py) and (pdb2pqr.py)
http://www.pymolwiki.org/index.php/Apbsplugin

And calculate the PQR at different pH?
http://www.poissonboltzmann.org/pdb2pqr/user-guide/using-pdb2pqr
Server
http://kryptonite.nbcr.net/pdb2pqr/

In the "Main" tab, in the APBS pymol plugin.
Select: "Choose Externally generated PQR".

Or use this:

python pdb2pqr.py --ff=AMBER --with-ph=5

As far as I know, pdb2pqr, uses PROPKA 1.0 to get the pKa.
There has been a large development to PROPKA since then.
Version 3.1 is available at homepage: http://propka.ki.ku.dk/

If you want to visualize the pKa, try this Pymol script.
http://www.pymolwiki.org/index.php/Propka


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2012/2/3 Xiaoshan Min <xsmin@yahoo.com>
Hi Pymoler,

I want to present a structure to non-structural biologist. They want to visualize the change of surface charge at different pH.  For example, Histidine will have different protonation state at pH 7.5 and 5.  What would be the best way to visualize this?  I know an accurate calculation probably is too hard, but would like to know if there is a clever way of approximation.

Thanks a lot.

Xiaoshan


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