Electrostatic potential maps: Difference between revisions
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[https://pymol.org PyMOL] has a license fee, but is free for students and educators. | [https://pymol.org PyMOL] has a license fee, but is free for students and educators. | ||
<ol> | |||
<li> Download and install PyMOL. | |||
<li> Enter command "fetch 1pgb". | |||
<ul> | |||
<li> The above command loads the asymmetric unit. Commands to load biological assembly 1: | |||
<li> fetch 7mgp, type=pdb1 | |||
<li> split_state 7mgp | |||
</ul> | |||
<li> Menu: All, Action, remove waters. | |||
<li> Menu: 1pgb, Action, generate, vacuum electrostatics, protein contact potential (local). | |||
<li> Enter command "bg_color white". | |||
</ol> | |||
Optional: The probe radius used to generate the molecular surface can be changed, and the previously generated surface will immediately change. The command is "set solvent_radius, 1.2" (don't overlook the comma!). | Optional: The probe radius used to generate the molecular surface can be changed, and the previously generated surface will immediately change. The command is "set solvent_radius, 1.2" (don't overlook the comma!). | ||
