How about using the APBS plugin?

The plugin that is shipped with Pymol as standard

The same plugin, but in the Pymol-script-repo
Here the plugin is setup to find the included ( and (

And calculate the PQR at different pH?

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

Or use this:

python --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:

If you want to visualize the pKa, try this Pymol script.

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2012/2/3 Xiaoshan Min <>
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.


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