Prime User Manual - ISP

Table 11.6. General keywords for the refinestruct script (Continued)
Keyword syntax Description
Chapter 11: Command Syntax
EXT_DIEL value Dielectric constant of the continuum solvation model. Default: 80.0.
Used with SGB_MOD sgbnp.
INT_DIEL value Dielectric constant used within the radius of an atom. Default: 1.0.
NUM_OUTPUT_STRUCT n Number of conformations to return for single loop refinements. This has
no effect on helix refinements or jobs composed of more than one refinement
(e.g. 2 loops, 1 helix + 1 loop, etc.). All structures are returned in a
single structure file in Maestro format. Default: 1.
PAIR_CONSTRAINT_i
atom1,atom2,value
Specify a constraint on a pair of atoms. The format of the atom specifications
is given at the beginning of this chapter. The value is the distance
between the atoms in angstroms.
PRIME_TYPE type Type of refinement to perform. The available options are:
SIDE_PRED Predict Side Chains (prefix SC)
LOOP_BLD Predict Loops and Helices
REAL_MIN Minimize Energy (prefix MINI)
SITE_OPT Active Site Minimization (including ligand)
ENERGY Energy Calculation
RESIDUE_i spec Specify a residue to refine. The numbering i begins at 0, and increases
incrementally. The format of the residue specification spec is given at
the beginning of this chapter.
RETAIN_CORRECTIONS
{yes | no}
Retain corrections made when duplicate residue numbers are found. The
duplications detected are between non-protein residues or between protein
and non-protein residues. The non-protein residue is assigned a new,
unique chain name temporarily. If you set this keyword to yes, the new
chain name is written to the output file. Default: no.
SEED n The integer to use as the seed for the random number generator if
USE_RANDOM_SEED is false. If it is true, SEED is ignored. Default: -1,
meaning that the program will generate a random seed rather than use
the supplied seed.
SELECT string Specify the manner for specifying which residues to refine. Available
options are:
all Refine all residues
pick Refine the specific residues, indicated by included
RESIDUE_i parameters (see above).
file Read list of residues to refine from a file. The file consists of a
series of lines with a residue specification on each line.
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