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2018-07-25T05:40:11Z

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2018-07-24T11:16:45Z

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[[Image:APBS-Electrostatics-Plugin-Options.png|right]]

The [[APBS Electrostatics Plugin]] integrates the
[http://www.poissonboltzmann.org APBS]
software package into PyMOL.
Its primary purpose is electrostatic surface visualization.
It superseedes the [[apbsplugin|APBS Tool2.1]] plugin.

''New in Incentive PyMOL 2.0''

== Usage ==

''A molecule must already be loaded into PyMOL.''

For regular protein and DNA molecules, the plugin should be a one-click solution (just click "Run").

For RNA, the residue names might need adjustment, see [[#RNA|troubleshooting RNA]].

Non-protein/DNA/RNA molecules or modified residues need special preparation, see [[#Prepare Molecule]].

== Procedure ==

The default procedure involves three steps:
# preparing the molecule by assigning partial charges and adding hydrogens and other missing atoms
# calculating the electrostatic map
# visualization of the charged molecular surface

Each step can be run individually by unchecking the checkboxes on the other steps.

=== Prepare Molecule ===

APBS requires '''partial charges''' and '''atom radii'''. Since PDB files
don't provide this information, they have to be preprocessed first.

'''pdb2pqr''' is the default preparation method, it is limited to protein and
nucleic acid, unless the user provides his own forcefield parameters.

The '''prepwizard''' method is available if the user has the
[https://schrodinger.com Schrodinger Suite]
installed. It can handle a variety of molecules.

You can also use any '''third-party tool''' that assigns partial charges
and load the result into PyMOL. Supported file formats include PQR, MOL2, and MAE.
In that case, uncheck "Prepare Molecule", or use
"Method: use vdw" if you only have charges but no radii.
Tools to consider are for example [http://openbabel.org/ Open Babel]
or the [http://www.poissonboltzmann.org/ PDB2PQR web server].

=== Calculate Map with APBS ===

* Focus Selection: If you only care about e.g. a binding site, you can specify a [[Selection Algebra|PyMOL selection]] here to speed up the calculation.

* Grid spacing (Angstrom): Increase to speed up the calculation and to reduce memory usage. Decrease to get a higher map resolution.

[[Image:ramp-levels-menu.png|thumb|right|changing ramp level after APBS calculation]]

=== Molecular Surface Visualization ===

The most common visualization is to show the solvent excluded surface.
PyMOL uses the [[surface_ramp_above_mode|potential at the solvent accessible surface]]
for coloring in that case.

The '''range''' (color intensity) can also be changed later once the result is in PyMOL.
Click "run01 > apbs_ramp01 > A > levels > ..." in the object menu panel.

== Troubleshooting ==

=== RNA ===

For '''pdb2pqr''', RNA resdiue names must be RA, RC, RG, and RU.

alter polymer & resn A+C+G+U, resn = "R" + resn

=== Incomplete Residues ===

Electrostatics should be analyzed on a complete molecule without missing
sidechains, and ideally without missing loops.
'''pdb2pqr''' will automatically model up to 10% of missing sidechain atoms.
If your structure is incomplete, consider creating a homology model first
using a tool of your choice (e.g. [https://salilab.org/modeller/ MODELLER]).

Some truncated PDB files include a single backbone atom of the next residue,
e.g. [https://www.rcsb.org/structure/2xwu 2xwu] chain B residue 954 atom N.
'''pdb2pqr''' reports:

<blockquote>
''Error encountered: Too few atoms present to reconstruct or cap residue LEU B 954 in structure!''
</blockquote>

The easiest solution is to remove that atom:

remove /2xwu//B/954

== APBS Template ==

Parameters like temperature, protein and solvent dielectric, or ion concentrations can be changed directly in the "APBS Template". Please read the [http://apbs-pdb2pqr.readthedocs.io/en/latest/apbs/input/ APBS input file documentation].

== Examples ==

=== RNA Molecule ===

fetch 1rna, async=0
alter polymer & resn A+C+G+U, resn = "R" + resn

* Open plugin
* click "Run"

=== Virus Assembly ===

set assembly, 1
fetch 3j7l, async=0
split_states 3j7l
delete 3j7l

* Open plugin
* Selection: 3j7l_*
* Calculate Map with APBS > Options >> Grid Spacing: 2.0
* click "Run" ''(takes about 20 minutes!)''

== See Also ==

* [[apbsplugin]]
* [[APBS]]
* [[ramp_new]] command

[[Category:Electrostatics]]
[[Category:Plugins]]

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