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110
Chapter 11: Command Syntax
Table 11.11. Keywords for the sta program.
Keyword syntax Description
QUERY_NAME name Name of the query sequence.
QUERY_FILE filename File name of the query sequence in FASTA format.
FORMAT string Alignment file format. Default is Maestro. Set to dev for plain text format—see
page 111 for an example.
BGNRES n The first residue of the query that is used in alignment. Default: 1.
ENDRES n The last residue of the query sequence that is used. Default: the last residue
of the original query sequence.
PREDSS[_i] filename Secondary structure prediction file of the query sequence, in CASP format.
One occurrence of this keyword is required for each file, and there
must be at least one SSP file specified. If only one prediction is used, the
keyword is PREDSS; if more predictions are used, the keyword is suffixed
with an index i, starting from zero: PREDSS_0, PREDSS_1, and so
on. For an example of CASP format, see page 93.
TEMPLATE_PDB filename Filename of the template structure, in PDB format.
MODE string Optional. Needed in the input file only when there are user-specified
constraints. In that case, the value is set to user.
PAIR pair-list Optional. User-specified residue pairing, used only when MODE is set to
user. All the residue pairs can be added after the keyword in one or
multiple lines. For example, the following lines pair residue 12, 20, 60
from the query sequence with residue 15, 24, 65 from the template.
MODE user
PAIR 12 15 20 24
PAIR 60 65
GAP gap-list Optional. User-specified gaps, used only when MODE is set to user. Can
be used with or without PAIR. Gaps are specified by the residues in
either query (P) or template (T) that are aligned with them. For example,
the following opens gaps against query residue 10, 11, template residue
34 and 35.
MODE user
GAP P10 P11 T34 T35
• Template PDB file—Template structure file, in PDB format. The sequence used for the
template is taken from SEQRES lines in the PDB file. If SEQRES is not found in the PDB
file, the template sequence is then taken from ATOM records.
• Output alignment file—File named jobname.out containing pairwise alignment between
the query and the template. By default, the alignment is in Maestro format. To generate
plain text format, include FORMAT dev in the command input file. In plain text format,
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