To use DIAL, you must either upload or give the 4 character alphanumeric PDB accession code for both query and target RNA structures, and indicate the chain identifier for each (underscore if the PDB file contains no chain identifier). Default weights for dihedral and pseudo-dihedral angles contributions to the alignment may be taken or modified.
You may choose between the global-semiglobal motif finding algorithm (default), or global or local alignment. If you choose to compute the Boltzmann pair probabilities (see helpBoltzmann), then three temperatures may be chosen for the pair probability computation to determine highly significant portions of the alignment.
This figure displays the output of DIAL, when executing global-semiglobal alignment of query 1J5A (chain A, nucleotides 2530 to 2536) with target 1HR2 (chain A). Note the hot links to obtain the alignment and Boltzmann probabilities, depicted in the output figure. Dihedral and pseudo-dihedralangles, sugar pucker, and other values, are computed by DIAL.
Output from DIAL for sample input is given here. The input target PDB file consists of only chain A of 1HR2i. The input query PDB file consists of only residues 2530 to 2536 of the A chain of 1J5A. When running DIAL on this example, you must enter chain A (upper or lower case) for both target and query.