Upload PDB file using "Choose File" option, or enter the 4-character alphanumeric PDB code for both the target and query. Chain ID must be specified in the appropriate field to the right (Chain and subsequence). In particular, DIAL will not recognize input of form 1ASZ:R to designate the R chain of aspartyl-tRNA PDB file.
Terms "query" and "target" are used, since the default DIAL algorithm is global-semiglobal alignment; i.e. the alignment is a global alignment of the query and a semi-global alignment of the target. In the case of global and local alignment, it is more common to speak of sequence/structure A and B, rather than query and target.
If the user wishes to use the motif detection (global-semiglobal) alignment algorithm for a fragmented query, then the query PDB file must contain different models, where MODEL 1 is the first contiguous portion of query, MODEL 2 is second contiguous portion of query, etc. This follows the format of the SCOR database (Klosterman PS, Tamura M, Holbrook SR, Brenner SE. 2002. SCOR: a structural classification of RNA database. Nucleic Acids Res. 30. 392-394.)