PURPOSE: Use this script to select atoms in the 3D window that were previously mapped to a query in the Ligand Pharmacophore Mapping protocol.

INSTALLATION INSTRUCTIONS: Save the script, ‘Select Mapped Atoms From Ligand Pharmacophore Mapping in 3D Window.pl’ to a local directory or location accessible from the Files Explorer

USAGE: From DS Client: Open a .sd file that was output from the Ligand Pharmacophore Mapping protocol into the Table Browser. There should be a column named MappedAtoms. This contains the atom numbers that mapped to the query in Ligand Pharmacophore Mapping.

Click on a row to display the aligned ligand. There should only be one ligand displayed at a time. To view the Mapped Atoms in the 3D window, run this script.

From the Files Explorer, double-click on the saved .pl file to launch the script. Or, right-click on the file and select Open With | Script Window then launch the script using the Run command from the Scripting toolbar.

You can also add the script to your Scripts pull-down menu, using the Script Commands subpage found in Edit/Preferences/General/Script Command.

DISCLAIMER: This custom script is compatible with Discovery Studio 2.0 and Discovery Studio 2.1. It is provided "as is" and is NOT supported by Accelrys nor is it warranted for any purpose whatsoever. The user assumes responsibility for any malfunctions or bugs.

The attached .zip contains:
1. The 'Select Mapped Atoms From Ligand Pharmacophore Mapping in 3D Window.pl' DiscoveryScript
3. A sample file called Trainingset-MetRS_Mapped_Atoms.sd. This file was output from a previous Ligand Pharmacophore Mapping run (DS 2.1).