Editing Mole:Plugins

=Informations=
 {{large| '''Notice:'''}} MOLE 2.5 extension requires MOLE 2.5 binary and the other way round MOLE 2.0 extension requires 2.0 binary! PyMOL 2.0 is presently not supported.

MOLE 2.5 provides a means how to take advantage of the MOLE algorithm in the environment of popular molecular browsers such as [http://pymol.org/ PyMOL] or [https://www.cgl.ucsf.edu/chimera/ UCSF Chimera]. Therefore, the results can be readily visualized and prepared for publication in high-quality figures. The extension is available for download [https://webchem.ncbr.muni.cz/Platform/AppsBin/Mole/2.5.17.4.24/Mole2_plugin.zip here].

 Please note, that running MOLE software on any other platform but Windows, requires [http://mono-project.com Mono] to be installed 

[[File:Mole-Plugin.png|500px|thumb|center|MOLE 2.5 plugin]]

=Working with the plugin=
* Start PyMol/Chimera from the writable directory
* Set up path to the '''working directory''', '''MOLE 2.5 executable''', ''optional:'' In case you are running MacOS or Linux(Unix), please specify '''mono executable.
* ''Optional:'' in order to get starting point suggestion from the CSA database, please specify CSA flat file location.
* Select input structure from the structure list
* Set calculation parameters
* Compute!

=Installation=
==PyMOL==
Installation of the MOLE 2.5 extension in the PyMOL environment is fairly simple. First, select in the PyMOL menu ''Plugin'' -> ''Plugin Manager''. Click ''Install New Plugin'' tab and select the *.zip directory with the programmatic extension. After the PyMOL restart, ''MOLE 2.5 extension'' can be found in the ''Plugin tab''. The entire process is highlighted at the following figures:

<gallery mode='packed-hover'>
File:PyMOL_plugin_install_1.png | Fig. 1
File:PyMOL_plugin_install_2.png | Fig. 2
</gallery>

==Chimera==
Installation of the MOLE 2.5 extension in the UCSF Chimera environment can be summarized in the following steps:
* Click 'Favorites tab' and select ''Add to Favorites/Toolbar'' (Fig. 1)
* Click 'Add button' and select parent directory with the unzipped extension archive (Fig. 2)

The MOLE 2.5 extension is available from the Tool icons menu by clicking on its icon and in the menu Tools->Surface/Binding Analysis-> MOLE 2.5

<gallery mode='packed-hover'>
File:Chimera_plugin_install_1.png | Fig. 1
File:Chimera_plugin_install_2.png | Fig. 2
File:Chimera_plugin_install_3.png | Fig. 3
</gallery>