Prime User Manual - ISP

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Chapter 11: Command Syntax
11.2 bldstruct—Build a Protein Model from an Alignment
The bldstruct script can be used to build initial (unrefined) protein models from an alignment
to one or more templates via the Protein Local Optimization Program (PLOP).
bldstruct handles all the tasks associated with the building of homology models via PLOP
(i.e. parsing and preparation of input files, interaction with PLOP, and handling of output structures,
etc.). All jobs handled by bldstruct are run under Schrödinger Job Control.
Multithreaded execution (with Open MP) can be enabled for bldstruct jobs by setting the
environment variable OMP_NUM_THREADS. It is recommended to set this environment variable
in the schrodinger.hosts file for hosts on which multithreading is supported—see
Section 6.1 of the Installation Guide.
Syntax
$SCHRODINGER/bldstruct input-file [input-file2 ...] [options]
The input file can be specified with or without the .inp extension. If multiple input files are
specified, the chains are combined to build a multimer. Each input file should correspond to a
single chain of the multimer, and be accompanied by the usual associated PDB template structure
and alignment files. The output is a single structure that contains all of the chains, refined
together; the job and the output file are named after the first input file.
Options
The -DEBUG and -HOST options are recognized by bldstruct. See Section 2.3 of the Job
Control Guide for more information.
Command Input File
The command input file is named jobname.inp. This input file contains keyword-value pairs,
one pair per line separated by one or more spaces. The keywords are given in Table 11.3.
Table 11.3. Keywords for the bldstruct script
Keyword syntax Description
BUILD_DELETIONS {true |
false}
BUILD_TRANSITIONS {true |
false}
Prime 2.1 User Manual
Turn on or off closure of the chain breaks near deletions in the
alignment. If not closed, they will remain as chain breaks in the
output structure. Default: true.
Turn on or off closure of the junctions between templates in multitemplate
homology modelling jobs. If not closed, they will remain
as chain breaks in the output structure. Default: true.