Changes

*Pymolhttp://pymol.sourceforge.net/*APBShttp://sourceforge.net/projects/apbs/ this may require a linux box (or can install via Cygwin)

===Generate PQR File and PX Files for the Structure===

#Go to the PDB2PQR server at http://pdb2pqr-1.wustl.edu/pdb2pqr/. THe The default settings (AMBER forcefield, internal naming scheme)are ok. Check off the Create an APBS input file button.#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.#Under molecular surface click '''Color by potential on sol. accesible surface'''.#Click on show and adjust settings to -10kV to 10kV and press show again. You may need to adjust these settings again depending on the charge state of your molecule.. [[Category: Structures]][[Category: PyMol]][[Category: Bioinformatics]]