Prime User Manual - ISP

Table 11.7. Protocol-specific keywords for the refinestruct script (Continued)
Keyword syntax Description
HELIX_BUILD
spec1/spec2
Files
Chapter 11: Command Syntax
In addition to the input structure file, defined by the value of STRUCT_FILE, and the job files
(the command input file jobname.inp, and the log file jobname.log), bldstruct produces
the following output file:
Return Value
Build the specified sequence as a helix. The format of the residue specifications
spec1 and spec2 is given at the beginning of this chapter. You
should include enough residues on either side of the helical region in the
loop prediction to ensure that sufficient flexibility is available to build
the loop.
MAX_CA_MOVEMENT value Specify the maximum distance that any alpha carbon atom in the loop
should be allowed to move during refinement. Omitting this parameter
indicates that no restriction should be applied.
RES_SPHERE value All side chains that lie within this distance of the loop will also be optimized
during refinement. This allows these nearby side chains to “react”
to the loop being predicted. Default 0.0.
MIN_OVERLAP value Fraction of van der Waals distance used to define a clash. Smaller values
allow structures with worse potential atomic overlaps to be generated.
Default: 0.70
SITE_OPT
LIGAND string Residue specification for the ligand.
NPASSES n Number of passes through side chain optimization of the protein residues
followed by minimization of the protein residues (including the
backbone). These two steps are repeated the specified number of times
before proceeding to optimization of the protein and the ligand.
Default: 2. Files written from Maestro have NPASSES set to 1.
jobname-out.mae Final structures, all in a single file.
refinestruct returns a value of 0 on successful completion, 17 for license errors, and 1
otherwise. All error messages are printed to the file jobname.log. There is no comprehensive
listing of possible errors as these can arise in a variety of programs and scripts.
Prime 2.1 User Manual 101