psico.electrostatics
Electrostatics (simple alternative to the APBS Tools Plugin)
2012 Thomas Holder
License: BSD-2-Clause
Functions
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Show electrostatic potential on surface (calculated with APBS). |
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Create electrostatic potential map with APBS. |
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Get and validate apbs executable. |
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Create a volume object from a map object with default coloring for electrostatic potential (similar to positive and negative isosurface). |
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Create a difference density volume object. |
- psico.electrostatics.apbs_surface(selection='all', maximum=None, minimum=None, map_name=None, ramp_name=None, grid=0.5, quiet=1, *, group_name=None, _self=...)[source]
Show electrostatic potential on surface (calculated with APBS).
Important: surface_color is a object property, so when calculating surface potential for different selections and visualize them all together, you should first split them into separate objects.
Usage
apbs_surface [ selection [, maximum [, minimum ]]]
Example
fetch 2x19, async=0 split_chains apbs_surface 2x19_A, 10 apbs_surface 2x19_B, 10
See Also
map_new_apbs, APBS Tools Plugin, isosurface, gradient, util.protein_vacuum_esp
- psico.electrostatics.map_new_apbs(name, selection='all', grid=0.5, buffer=10.0, state=1, preserve=0, exe='', assign=-1, focus='', quiet=1, _template='', *, _self=...)[source]
Create electrostatic potential map with APBS.
For more control over parameters and a graphical user interface I recommend to use the APBS Tools Plugin instead.
In case of missing atoms or residues I recommend to remodel the input structure with modeller before calculating the electrostatic potential.
If selection has no charges and radii, they will be automatically assigned with PyMOL (not with pdb2pqr).
See Also
apbs_surface, map_new (coulomb), APBS Tools Plugin
- psico.electrostatics.validate_apbs_exe(exe)[source]
Get and validate apbs executable. Raise CmdException if not found or broken.
- psico.electrostatics.volume_esp(name, map, stops=(0.1, 1.0), neg='red', pos='blue', opacity=0.2, quiet=1, *, _self=...)[source]
Create a volume object from a map object with default coloring for electrostatic potential (similar to positive and negative isosurface).
Arguments
name = string: name for the new volume object
map = string: name of the map object to use
stops = list of floats: 2 or 3 values in standard deviations for creating the volume ramp {default: [0.1, 1.0]}
neg = string: color for negative volume {default: red}
pos = string: color for positive volume {default: blue}
opacity = float: maximum opacity in volume ramp {default: 0.2}
See Also
volume