PURPOSE: Reads a protein molecule from the last active 3D window and sequence alignment from the last active sequence window. The 3D window should contain the template structure and the sequence window should contain the template sequence as well as a model sequence. The script will loop over all residues in the template and mutate any residue that is aligned to a residue in the model sequence that is not of the same amino acid type. Template residues which are aligned to gaps in the model sequence may optionally be deleted.

INSTALLATION: Save manual_homology_modeling.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 manual_homology_modeling.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: The new structure is renamed to the model sequence name. The resulting 3D window will contain the original template as well as the model structure. A new group called "Mutated Residues" is defined for the model structure. The resulting Sequence Window will contain the sequences of both structures as they were originally aligned.

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