Generating and Displaying an Electostatic Surface: Difference between revisions
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#Go to plugin -> apbs tools -> visualization. | #Go to plugin -> apbs tools -> visualization. | ||
#Go to the visualization tab. | #Go to the visualization tab. | ||
#Click on show and adjust settings to -10kV to 10kV and press show again. | #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: Structures]] | ||
[[Category: PyMol]] | [[Category: PyMol]] | ||
[[Category: Bioinformatics]] | [[Category: Bioinformatics]] | ||
Revision as of 15:38, 18 November 2009
Programs Required
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 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..