PyMOLProbity - Revision history

Cchem: 1 revision

2019-04-29T03:23:33Z

1 revision

Speleo3: conda

2019-04-25T10:40:44Z

conda

Cchem: 4 revisions

2017-02-06T03:04:56Z

4 revisions

Jaredsampson: /* Description */ add link to repository

2017-01-16T04:19:26Z

Description: add link to repository

Jaredsampson: /* Getting Started */ Update GUI section.

2017-01-14T17:48:13Z

Getting Started: Update GUI section.

Jaredsampson: Add screenshot.

2017-01-14T17:41:55Z

Add screenshot.

Jaredsampson: Created page.

2017-01-14T05:52:15Z

Created page.

New page

{{Infobox script-repo
|type = plugin
|download = https://github.com/jaredsampson/pymolprobity/raw/master/pymolprobity.tar.gz
|author = [[User:jaredsampson|Jared Sampson]]
|license = MIT
}}

== Description ==
[[Image:PyMOLProbity_GUI.png|480px|thumb|The PyMOLProbity GUI can be used to inspect and adjust clashes and flip orientations of flippable side chain groups.]]

PyMOLProbity is a plugin allows the user to produce MolProbity-style
visualization of atomic interactions within a structure (e.g. H-bonds, van der
Waals interactions and clashes) directly within a PyMOL session. The plugin
runs local copies of several executable programs from the
[http://kinemage.biochem.duke.edu/ Richardson Lab] at Duke University,
authors of the [http://molprobity.biochem.duke.edu/ MolProbity] software, parses the output, and
displays the results in the PyMOL viewport. There are both a graphical user
interface (GUI) for general point-and-click use, and a command-line interface
(CLI) suitable for scripting.

== Installation ==

For installation instructions, please see the [https://github.com/jaredsampson/pymolprobity/blob/master/README.md README] file in the
[https://github.com/jaredsampson/pymolprobity repository].

== Getting Started ==

=== First run ===

Now you can open PyMOL, load or fetch a structure, and launch PyMOLProbity from
the Plugin menu.

* Use the ''Add Hydrogens'' tab to add hydrogens with Reduce. This will also calculate which N/Q/H residue side chains should be flipped.
* If you would like to examine these more closely, use the ''Review Flips'' tab to examine each flippable residue and choose the ones you wish to flip or keep.
* Save these using the ''Save Selections'' button.
* Finally, use the ''Visualize Contacts'' tab to run Probe on the modified coordinates and generate contact dots and clash vectors for all the atoms in your object.

=== Command-Line Interface ===

The plugin makes the following functions available:

* '''reduce_obj'''(obj, flip=1): Run reduce on a loaded PyMOL object (or named selection) with (default) or without making the Asn/Gln/His flips recommended by Reduce.

* '''flipkin_obj'''(obj): Run Flipkin to create both NQ and H flipkin kinemage visualization of the Reduce-modified structure.

* '''probe_obj'''(obj): Run Probe on either a structure saved from the Flipkin tab of the GUI, or the Reduce-modified structure.

Note that both `flipkin_obj` and `probe_obj` require previously having run `reduce_obj` on the same object.

[[Category:Plugins]]

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 For installation instructions, please see the [https://github.com/jaredsampson/pymolprobity/blob/master/README.md README] file in the
 [https://github.com/jaredsampson/pymolprobity repository].
 == Getting Started ==

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 [[File:PyMOLProbity_GUI.png|480px|thumb|right|The PyMOLProbity GUI can be used to inspect and adjust clashes and flip orientations of flippable side chain groups.]]
-PyMOLProbity is a plugin allows the user to produce MolProbity-style
+[https://github.com/jaredsampson/pymolprobity PyMOLProbity] is a plugin allows the user to produce MolProbity-style
 visualization of atomic interactions within a structure (e.g.  H-bonds, van der
 Waals interactions and clashes) directly within a PyMOL session.  The plugin

@@ Line 26: / Line 26: @@
 == Getting Started ==
-=== First run ===
+=== GUI ===
-Now you can open PyMOL, load or fetch a structure, and launch PyMOLProbity from
+Once PyMOLProbity is installed, it should appear as an option in PyMOL's ''Plugin'' menu.  Load or fetch a structure, and launch the GUI by selecting ''Plugin > PyMOLProbity''.
-* Use the ''Add Hydrogens'' tab to add hydrogens with Reduce. This will also calculate which N/Q/H residue side chains should be flipped.
+* Use the ''Add Hydrogens'' tab to add hydrogens with Reduce. This will also calculate which N/Q/H residue side chains should be flipped, and perform those flips.  Note that this should be done even if the model already includes explicit hydrogens.
-* If you would like to examine these more closely, use the ''Review Flips'' tab to examine each flippable residue and choose the ones you wish to flip or keep.
+* To examine these more closely, select the ''Review Flips'' tab.  Here, you can zoom to inspect each flippable residue and choose the ones you wish to keep or change.  Save any changes using the '''''Save Selections''''' button.
 * Finally, use the ''Visualize Contacts'' tab to run Probe on the modified coordinates and generate contact dots and clash vectors for all the atoms in your object.

@@ Line 7: / Line 7: @@
 == Description ==
-[[Image:PyMOLProbity_GUI.png|480px|thumb|The PyMOLProbity GUI can be used to inspect and adjust clashes and flip orientations of flippable side chain groups.]]
+[[File:PyMOLProbity_GUI.png|480px|thumb|right|The PyMOLProbity GUI can be used to inspect and adjust clashes and flip orientations of flippable side chain groups.]]
 PyMOLProbity is a plugin allows the user to produce MolProbity-style