Spruce TK Examples

The following table lists the currently available Spruce TK examples:

Program	Description
make_design_units	constructing design units from a PDB (due to loop modeling this example takes ~10 min)
make_apo_design_units	constructing apo design units from a PDB using a site residue input (due to loop modeling this example takes ~10 min)
simplesuperposition	simple superposition of two proteins
secondarystructuresuperposition	secondary structure superposition of two proteins
extract_biounits_remarks	extract biounits from PDB header remarks
extract_biounits_ref	extract biounits from a sequence alignment to a reference protein

Examples:

• Creating OEDesignUnits from a PDB file
• Creating apo OEDesignUnits from a PDB file
• Calculating simple superposition
• Calculating secondary structure superposition
• Extracting Biounits from PDB header remarks
• Extracting Biounits by aligning to a reference protein