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<http://www.pymolwiki.org/index.php/Git_intro>
.
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
Troels Emtekær Linnet
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2012/2/3 Xiaoshan Min <xs...@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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