Difference between revisions of "Generating and Displaying an Electostatic Surface"
From Bridges Lab Protocols
Davebridges (Talk | contribs) (Created page with '==Programs Required== *Pymol *APBS ===Generate PQR File for the Structure=== #Download or generate PDB file. #Go to the PDB2PQR server at http://pdb2pqr-1.wustl.edu/pdb2pqr/. T...') |
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==Programs Required== | ==Programs Required== | ||
| − | *Pymol | + | *Pymol http://pymol.sourceforge.net/ |
| − | *APBS | + | *APBS http://sourceforge.net/projects/apbs/ this may require a linux box (or can install via Cygwin) |
| − | ===Generate PQR | + | ===Generate PQR and PX Files for the Structure=== |
#Download or generate PDB file. | #Download or generate PDB file. | ||
| − | #Go to the PDB2PQR server at http://pdb2pqr-1.wustl.edu/pdb2pqr/. | + | #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. | + | #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]] | ||
Latest revision as of 15:46, 18 November 2009
Programs Required
- Pymol http://pymol.sourceforge.net/
- APBS http://sourceforge.net/projects/apbs/ this may require a linux box (or can install via Cygwin)
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..
