The PDB2PQR web portal provides support for the execution of PDB2PQR and APBS as well as the visualization of the resulting electrostatic potentials. We will provide a basic demonstration of how to go from a PDB entry to a plot of structure & potential through the PDB2PQR web portal.
We'll perform this example with Fusarium solani cutinase (PDB ID 1CUS) a lipolytic enzyme with a catalytic serine accessible to solvent.
First go to the PDB2PQR web portal, enter a PDB ID or upload a PDB file, choose your options for PDB2PQR, then click "Submit"
On the PDB2PQR result page, click bottom link to run APBS with your results.
On the APBS web solver page, click "Launch" to use default parameters for APBS calculation; or, if you prefer to run APBS with custom parameters, check the check box and make your own selections.
Wait until the calculation is complete, click the bottom link to visualize your results.
Configure your visualization, then click "Submit"
Please be patient and wait until the visualization applet is fully loaded.
±5 kT/e electrostatic potential of 1CUS rendered on the molecular surface. Figure made through Jmol.
Jmol also has the ability to generate scenes for higher-quality offline rendering with POV-Ray. This is particularly useful for transforming the images you generate with Jmol via the PDB2PQR web server into high-resolution figures for publication. These instructions assume that you have POV-Ray installed.
Set up the scene in Jmol to look the way you would like the rendered image to appear.
Right click on the Jmol window and select File -> Export POV-Ray Image.
Save the resulting
Run POV-Ray and load up the
Once you've finished editing, click the POV-Ray "Run" button to render your image.