From WebChem Wiki
Revision as of 18:11, 19 July 2017 by Lukas (talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


 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 PyMOL or UCSF Chimera. Therefore, the results can be readily visualized and prepared for publication in high-quality figures. The extension is available for download here.

Please note, that running MOLE software on any other platform but Windows, requires Mono to be installed 
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 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 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