The following table shows arguments that are required when scripting a local Nova application prediction. Only a subset of these arguments is required, depending on the application. The three rightmost columns show whether the argument applies to NF (NovaFold), NFA (NovaFold Antibody) or ND (NovaDock).
|Name||Definition||Arguments and Defaults||NF||NFA||ND|
|--datadir DATADIR||The path to the location where output/results will be written.||✔||✔|
|--seqname SEQNAME||The unique name of the query sequence.||✔||✔|
|--output-dir OUTPUT, -o OUTPUT||The path to the result output directory.||✔|
|--name NAME||The name for this complex prediction.||✔|
|--lfile LFILE||Path to a ligand PDB file that includes all chains. The ligand is often, though not always, smaller than the receptor.||✔|
|--rfile RFILE||Path to a receptor PDB file that includes all chains. The receptor is often, though not always, larger than the ligand.||✔|
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