PURPOSE: Given a trajectory/conformations msv file (loaded into the DS Client) in which some atoms or residues have been selected, this script will loop through each conformation and report the Solvent Accessible Surface Area for those selected atoms in that conformation. The areas (in Angstrom^2) are reported in the Output view as well as a new column in the Conformation tab titled "SAS of Selected Atoms". The user has the option to modify the probe radius, see line #40 in the .pl script.

INSTALLATION: Save surface_selectedatoms_trajectory.pl to a local directory or location accessible from the Files Explorer

USAGE: From the DS Client: From the Files Explorer, double-click on the surface_selectedatoms_trajectory.pl 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.

DISCLAIMER: This custom script is compatible with 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.

EXPECTED RESULTS: Surface areas for each conformation are reported in the Output View of the Script Window. The Conformation tab of the active 3D window will contain a new column with the heading "SAS of Selected Atoms" in which the values of the calculated areas will be stored.

The attached .zip contains:
1. A README.txt
2. The surface_selectedatoms_trajectory.pl DiscoveryScript