Prime User Manual - ISP

Table 11.3. Keywords for the bldstruct script (Continued)
Keyword syntax Description
Chapter 11: Command Syntax
COMPOSITE_ARRAY string A string of integers indicating from which template (or, more specifically,
from which alignment) coordinates for a given residue
should be obtained. Thus, this string of integers must be equal in
length to the query sequence being used in the alignment files.
COMPOSITE_ARRAY is required for multiple template jobs. It is not
required for single template jobs, but if it is present, it is ignored.
KEEP_ROTAMERS {true |
false}
Specifies which side chains to optimize. If true, the rotamers for
conserved side chains are preserved, and only non-conserved side
chains are predicted. If false, all side chains are predicted. This
keyword is ignored if SIDE_OPT is false. Default: true.
MAX_INSERTION_SIZE n Specifies the longest insertion in the alignment that will be built.
Insertions longer than this will be omitted, and not appear in the
output structure. Residue numbering will reflect the full query
sequence however. Default: 1000.
MINIMIZE {true | false} Turn on or off minimization of regions that were not directly copied
from the template structure. These regions primarily include portions
of the structure involved in closing gaps or building insertions,
but also include any side chains optimized due to the
SIDE_OPT keyword. Default: true.
SIDE_OPT {true | false} Turn on or off a side chain optimization stage. Default: true.
template_ALIGN_FILE
filename
template_HETERO_i
ligand-spec
Required. The name of the file containing the alignment between
this template and the query. Details on the format are provided in
the Examples section below.
Required if a ligand is present. Specifies a ligand to include from
this template. The format of the specification is
AAA C:###
where AAA is the ligand’s three letter code, C is its chain ID, ### is
its residue number. Multiple ligands from the template are numbered
using i as an index, starting from zero.
TEMPLATE_NAME template Required. A label used to identify a given template in subsequent
data fields. For example, if TEMPLATE_NAME is set to 1BPJ_A,
other template-specific fields are given as 1BPJ_A_STRUCT_FILE,
1BPJ_A_ALIGN_FILE, and so on.The chain to be used is specified
by an underscore and letter suffix: for example, for 1BPJ_A, chain
A will be used. The chain suffix must be included in the label.
template_NUMBER n Required. Used to identify a given template in the
COMPOSITE_ARRAY (see below). Numbering goes from 1 to 9.
Prime 2.1 User Manual 89