Hi there, I'm trying to use DS 3.0 to determine a moleclue's pH vs. charge relationship. I'm taking a PDB file (for example, 1HLG), loading it into DS, then running "Prepare Protein" with different pH's. According to Brockerhoff and Jensen, 1974, the isoelectric point for 1HLG (human gastric lipase A) is 4.9. But this is the plot that I generated from the data I collected:

The charge was determined by using the sum of the formal charges, which I obtained with this script:

#!/usr/bin/perl -w

use strict;

use MdmDiscoveryScript;

use MdmCommands;

my \$document = FileOpen('1HLG.dsv');

my \$proteins = GetProteinMolecules(\$document);

foreach my \$protein (@\$proteins)

{

    # Print name

    print \$protein->FormalChargeSum

}

I was able to replicate this issue with other molecules, as well as with single amino acids. At the expected isoelectric point, the charge was always around 10-20, when it should have been 0. Does anyone know what I'm doing wrong here?

I also tried accessing the sum of the formal charges via the table below the main pane, but it wasn't accessible by default. If someone knows how to make the addition of the sum of formal charges parameter to the table below the main pane permanent, I'd like to know that as well.

Thanks!