Difference between revisions of "Generating and Displaying an Electostatic Surface"

Revision as of 00:52, 10 October 2009

Download or generate PDB file.
Go to the PDB2PQR server at http://pdb2pqr-1.wustl.edu/pdb2pqr/. The default settings (AMBER forcefield, internal naming scheme), are ok. Check off the prepare APBS input file.
Save the pqr file and the APBS input file.
Run APBS as apbs inputfile.in. This will generate a *.dx file.

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 ==Programs Required==
-*Pymol
+*Pymol http://pymol.sourceforge.net/
-*APBS
+*APBS http://sourceforge.net/projects/apbs/
-===Generate PQR File for the Structure===
+===Generate PQR and PX Files for the Structure===
 #Download or generate PDB file.
-#Go to the PDB2PQR server at http://pdb2pqr-1.wustl.edu/pdb2pqr/.  The default settings (AMBER forcefield, internal naming scheme), are ok.  Check off the prepare APBS input file
+#Go to the PDB2PQR server at http://pdb2pqr-1.wustl.edu/pdb2pqr/.  The default settings (AMBER forcefield, internal naming scheme), are ok.  Check off the prepare APBS input file.
 #Save the pqr file and the APBS input file.
+#Run APBS as '''apbs inputfile.in'''.  This will generate a *.dx file.
+===Visualizing Electrostatic Surface===
+#Open pdb file then dx file in pymol.
+#Go to plugin -> apbs tools -> visualization.
+#Go to the visualization tab.
+#Click on show and adjust settings to -10kV to 10kV and press show again.
 [[Category: Structures]]
 [[Category: PyMol]]
 [[Category: Bioinformatics]]