As an input for our "SCWRL for AS2TS" processing the protein structure in PDB format is required (at least mainchain ATOM coordinates).
By default, for a given PDB model SCWRL program calculates all sidechain atoms for all amino-acids.
Our AS2TS system offers a user an option to select a PDB template which will serve as a STATIC_FRAME for SCWRL calculations. After selecting a name of the template chain from PDB (e.g. 1wdn_A), or attaching to the PDB model the following line:
REMARK Templates: 1wdn_A or REMARK Sbjct= 1wdn_Athe LGA program will structurally align PDB model to the selected template (in this example PDB entry: 1wdn chain A), the identical residues will be identified, and AS2TS system will copy atom coordinates from the corresponding residues from the template to the model. In this case SCWRL program will be used only to build sidechain atoms for remaining (not aligned) residues.
NOTE: Standard amino-acids and ATOM records only are processed by this version of the system.
References:  Bower, M., Cohen, F. E., Dunbrack, Jr. R. L. (1997). "Sidechain prediction from a backbone-dependent rotamer library: A new tool for homology modeling", J. Mol. Biol. 267, 1268-1282.  Canutescu, A. A., Shelenkov, A. A., and Dunbrack, Jr. R. L. (2003). "A graph theory algorithm for protein side-chain prediction", Protein Science 12, 2001-2014.