Mole:Plugins - Revision history

Lukas at 08:32, 22 October 2017

2017-10-22T08:32:14Z

← Older revision		Revision as of 08:32, 22 October 2017
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	=Informations=		=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!		{{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].		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].

Lukas at 15:11, 19 July 2017

2017-07-19T15:11:42Z

← Older revision		Revision as of 15:11, 19 July 2017
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	==Chimera==		==Chimera==
	Installation of the MOLE 2.5 extension in the UCSF Chimera environment ~~is a bit complicated, but~~ can be summarized in the following steps:		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 'Favorites tab' and select ''Add to Favorites/Toolbar'' (Fig. 1)
	* Click 'Add button' and select parent directory with the unzipped extension archive (Fig. 2)		* Click 'Add button' and select parent directory with the unzipped extension archive (Fig. 2)

Lukas: /* Chimera */

2017-07-18T06:48:27Z

Chimera

← Older revision		Revision as of 06:48, 18 July 2017
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	* Click 'Favorites tab' and select ''Add to Favorites/Toolbar'' (Fig. 1)		* 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)		* Click 'Add button' and select parent directory with the unzipped extension archive (Fig. 2)
	* Open IDLE console from the following location ''Tools'' -> ''General Controls'' -> ''IDLE'' (Fig. 3)
	* Type in ''import FolderName'' (e.g. ''import MOLE2_5'') in the IDLE console and press ''Enter''.

	The MOLE 2.5 extension is available from the Tool icons menu by clicking on its icon.		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'>		<gallery mode='packed-hover'>

Lukas at 06:28, 18 July 2017

2017-07-18T06:28:01Z

← Older revision		Revision as of 06:28, 18 July 2017
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	[[File:Mole-Plugin.png\|500px\|thumb\|center\|MOLE 2.5 plugin]]		[[File:Mole-Plugin.png\|500px\|thumb\|center\|MOLE 2.5 plugin]]

	~~=Installation=~~

	=Working with the plugin=		=Working with the plugin=
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	* Compute!		* Compute!

			=Installation=
	==PyMOL==		==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:		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:

Lukas at 15:43, 17 July 2017

2017-07-17T15:43:01Z

← Older revision		Revision as of 15:43, 17 July 2017
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			=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!		{{large\| '''Notice:'''}} MOLE 2.5 extension requires MOLE 2.5 binary and the other way round MOLE 2.0 extension requires 2.0 binary!

	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 here.		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].

	=PyMOL=		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]]

			=Installation=

			=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!

			==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:		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:

Line 11:		Line 26:
	</gallery>		</gallery>

	=Chimera=		==Chimera==
	Installation of the MOLE 2.5 extension in the UCSF Chimera environment is a bit complicated, but can be summarized in the following steps:		Installation of the MOLE 2.5 extension in the UCSF Chimera environment is a bit complicated, but can be summarized in the following steps:
	* Click 'Favorites tab' and select ''Add to Favorites/Toolbar'' (Fig. 1)		* Click 'Favorites tab' and select ''Add to Favorites/Toolbar'' (Fig. 1)

Lukas: Created page with " {{large| '''Notice:'''}} MOLE 2.5 extension requires MOLE 2.5 binary and the other way round MOLE 2.0 extension requires 2.0 binary! MOLE 2.5 provides a means how to take ad..."

2017-07-12T14:53:19Z

Created page with " {{large| '''Notice:'''}} MOLE 2.5 extension requires MOLE 2.5 binary and the other way round MOLE 2.0 extension requires 2.0 binary! MOLE 2.5 provides a means how to take ad..."

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{{large| '''Notice:'''}} MOLE 2.5 extension requires MOLE 2.5 binary and the other way round MOLE 2.0 extension requires 2.0 binary!

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 here.

=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 is a bit complicated, but 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)
* Open IDLE console from the following location ''Tools'' -> ''General Controls'' -> ''IDLE'' (Fig. 3)
* Type in ''import FolderName'' (e.g. ''import MOLE2_5'') in the IDLE console and press ''Enter''.

The MOLE 2.5 extension is available from the Tool icons menu by clicking on its icon.

<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>