Prime User Manual - ISP

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Chapter 11: Command Syntax
11.5 refinestruct—Refine a Protein Structure
The refinestruct script runs protein structure refinement jobs (side chain prediction and
energy minimization as well as loop and helix prediction) using the Protein Local Optimization
Program (PLOP).
refinestruct handles all the tasks associated with the refinement of protein structures via
PLOP: parsing and preparation of input files, interaction with PLOP, and handling of output
structures, etc. It also fixes the structural issues that are fixed by primefix.py (see
Section 12.3 on page 118). All jobs handled by refinestruct 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/refinestruct [options] jobname
The input is read from the file jobname.inp and the structural output is written to the file
jobname-out.mae. If the input structure file has alternate coordinates, the refinement is
performed on the first set of alternate coordinates.
Options
The refinestruct script accepts the options listed in Table 11.1.
Command Input File
The command input file contains a list of keywords that control the operation of the
refinestruct script, one per line. The keywords are listed in the tables below. Generally
valid keywords are listed in Table 11.6 and protocol-specific keywords are listed in Table 11.7,
under the protocol to which they apply.
Table 11.6. General keywords for the refinestruct script
Keyword syntax Description
ECUTOFF value Energy cutoff for return of conformations. Returns all conformations
within value kcal/mol of the lowest-energy structure. It can be used in
conjunction with NUM_OUTPUT_STRUCT, to impose a maximum on the
number of such conformations to return. As with
NUM_OUTPUT_STRUCT, it only applies to single loop refinements.
Prime 2.1 User Manual