Editing Bondpack

{{Infobox script-repo
|type      = plugin
|download  = https://github.com/rasbt/BondPack
|author    = Sebastian Raschka
|license   = GNU GENERAL PUBLIC LICENSE
}}

== BondPack ==


A collection of PyMOL plugins to visualize atomic bonds.<br>



== Introduction ==
PyMOL is without any doubt a great tool to visualize protein and ligand molecules.<br>
However, drawing interactions between atoms can be often quite cumbersome when done manually.<br>
For the sake of convenience, I developed three plugins for PyMOL that will make our life as protein biologists a little bit easier.<br>
All three PyMOL plugins can be installed and used separately; they don't depend on each other, but rather complement each other.<br>
At the end of this article, you will find brief instructions on how to install plugins in PyMOL - a very quick and simple process.<br> 

== HydroBond ==
HydroBond visualizes all potential polar contacts between protein and ligand molecules within a user-specified distance.<br>  
The underlying function is based on the different atom types, such as hydrogen bond acceptor and donor atoms,<br>
and thus it is required to have hydrogen atoms present in the structure. <br>
If your structure file doesn't contain hydrogen atoms already, you can add them directly in PyMOL as shown in the image below.<br><br>
[[File:add_hydrogens.png]]
<br><br>HydroBond is related to PyMOLs "[A]->find->polar contacts" command, however,<br>
it doesn't consider geometry criteria and angle thresholds,<br> but is rather based on atom types.<br> 
When you select HydroBond from the "Plugin" menu, you will be prompted to enter the name of the protein object,<br>
the ligand object, and a distance cutoff as shown in the figure below.<br>
If HydroBond was able to detect hydrogen bond and acceptor atoms within the<br>
specified distance, potential interactions will be visualized as yellow dashed lines.<br><br>
[[File:hydrobond_action.png]]
<br><br>

== BondVis ==
The BondVis plugin lets you visualize interactions between any pair of atoms you specified.<br> 
Often I find it helpful for my understanding (and for verification) to visualize the bonds between certain atoms<br>
that were assigned in docking or any other prediction software.<br>
Most software will provide you with information about the atoms that were "connected" to perform the analysis.<br>
If you run BondVis from the "Plugin" menu, it will ask you to select a "bond info file."<br><br>
[[File:bondinfo.png]]
<br><br>
This is just a simple text file that contains the atom numbers of connected atoms in pairs.<br>
Those can be separated by spaces, tabs, or commas. An example file with bond information could look like this:<br> 
<code><pre>1174		1357
1175		1358
1176		1359
</pre></code>
<br>
When you selected a "bond info" file, BondVis will connect all atom pairs by yellow dashed lines<br>
and print out the connected atoms in the command field.<br><br>
[[File:bondvis.png]]
<br><br>

== BondLab ==
If you are not happy with the looks of the lines that were drawn to visualize connections between atoms,<br>
you will like to use BondLab.<br> This plugin offers a simple interface that allows you to change the diameter,<br>
gap width, and color of the lines. <br><br>
[[File:bondlab.png]]<br>
The following video demonstrates the different features of BondLab:<br>
http://youtu.be/14UZctxtK3w
<br>
== Github ==
If you are interested, you can follow the BondPack Github repository<br>
https://github.com/rasbt/BondPack for updates

[[Category:Script_Library]]
[[Category:Structural_Biology_Scripts]]
[[Category:Plugins]]