Generating and Displaying an Electostatic Surface: Difference between revisions
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==Programs Required== | ==Programs Required== | ||
*Pymol http://pymol.sourceforge.net/ | *Pymol http://pymol.sourceforge.net/ | ||
*APBS http://sourceforge.net/projects/apbs/ | *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=== | ===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/. The default settings (AMBER forcefield, internal naming scheme) are ok. Check off the | #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. | #Save the pqr file and the APBS input file. | ||
#Run APBS as '''apbs inputfile.in'''. This will generate a *.dx file. | #Run APBS as '''apbs inputfile.in'''. This will generate a *.dx file. | ||
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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]] | ||