Spanner is a structural homology modeling program―that is, it threads a specific amino-acid sequence onto a specific PDB structure, patching up the gaps as best it can.
To create a model, you must provide a template structure, as well as an alignment of the sequence you wish to model onto the template sequence. Spanner will replace matching residues, fill any gaps caused by inserted or deleted residues, and thermodynamically optimize the resulting structure.
The resulting PDB, as well as a log file, will be emailed to you when the modeling task finishes. If an error prevented a homology model from being generated (for example, when the alignment you provided does not match the template structure), the log file will explain which part of the modeling sequence failed.