PURPOSE: In DS 2.0, the Structure | RMSD commands allow you to calculate the RMSD between all atoms, all heavy atoms, and a variety of biopolymer structures. However, it does not include an option to calculate the RMSD between any 2 subsets of atoms.
The attached script provides that capability. It will work on any 2 groups of atoms as long as both groups contain the same number of atoms. Note, the RMSD is calculated by pairing up atoms as they appear listed in each group. If, for some reason, the atoms do not appear in the same corresponding order in each molecule, the calculated RMSD will be incorrect. In other words, this script does not verify atom names or chemistry.
INSTALLATION INSTRUCTIONS: Save rmsd_atom_groups.pl to a local directory or location accessible from the Files Explorer
USAGE: This script is intended for use from the DS Client and will act on the most recently accessed 3D Window.
Before executing this script, select 2 defined groups from the Hierarchy view. From the Files Explorer, right-click on the file and select Open With | Script Window then launch the script using the Run command from the Scripting toolbar. The calculated RMSD will be reported in the Output portion of the Script Window.
REQUIREMENTS: An open 3D window in which 2 groups (containing the same number of atoms) have been selected.
DISCLAIMER: This custom script is compatible with Discovery Studio 2.0. 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: When this script is executed on the sample .msv file included in the attachment, the following message will be reported in the Output portion of the Script Window:
"The RMSD between atoms in abb and sbb is 0.0706144403989901"
The attached .zip contains:
1. A README.txt
2. The rmsd_atom_groups.pl DiscoveryScript
3. A sample input file called dnatest.msv which has 2 groups already selected and is ready to have rmsd_atom_groups.pl executed on it.
