Download MODELLER A Program for Protein Structure

2.3. HANDLING OF ATOMIC COORDINATES
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# Example for: REORDER_ATOMS
# This will standardize the order of atoms in the model.
# Order the atoms according to a topology library:
READ_TOPOLOGY FILE = ’$(LIB)/top_heav.lib’
READ_MODEL FILE = ’1fas’
REORDER_ATOMS
WRITE_MODEL FILE = ’1fas.ini1’
2.3.15
ROTATE DIHEDRALS — change dihedral angles
Options:
DIHEDRALS = hstring : 0i
’PHI’ ’PSI’ ’CHI1’ ’CHI2’
’CHI3’ ’CHI4’
CHANGE = hstring : 1i
’RANDOMIZE’
DEVIATION = hreal : 1i
0.0
RAND SEED = hinteger : 1i
8123
dihedral angle type selection: ’phi’ |
’psi’ | ’omega’ | ’chi1’ | ’chi2’ |
’chi3’ | ’chi4’ | ’chi5’ | ’alpha’
what to do: ’RANDOMIZE’ | ’OPTIMIZE’
amplitude of dihedral angle randomization
random seed from -50000 to -2
Requirements:
for CHANGE=’OPTIMIZE’: topology & MODEL & restraints
for CHANGE=’RANDOMIZE’: topology & MODEL
Description: This command changes the dihedral angles in MODEL.
CHANGE selects an optimization (when equal to ’OPTIMIZE’) or randomization (when equal to ’RANDOMIZE’):
1. When optimizing, this command finds the first selected restraint that restrains the specified dihedral
angle of each selected residue. It then sets the value of that dihedral to the most likely value. A residue
is selected if any of its atoms is in the set 1 of selected atoms.
2. When randomizing, the command changes the specified dihedral angle of each selected residue by adding
a random value distributed uniformly from −DEVIATION to +DEVIATION degrees. The value of the
random seed variable, RAND SEED, is changed after returning from the RANDOMIZE command. Use a
negative integer from −2 to −50000 as the seed for the random number generator.
DIHEDRALS can be either a vector of dihedral angle names or a single string containing all the dihedral angle
names separated by blanks. The dihedral angles involved in cyclic structures are not changed (e.g., sidechain
dihedral angles in disulfide bonds and prolines). The dihedral angles that can be changed are listed at the top
of the $RESDIH LIB library: alpha, phi, psi, omega, chi1, chi2, chi3, chi4, chi5. Dihedral angle
’alpha’ is the virtual Cα dihedral angle defined by four consecutive Cα atoms.
The bond connectivity of the MODEL has to exist before this command is executed. If you read in the model
by READ MODEL, the bond connectivity is defined by subsequent calls to READ TOPOLOGY and
GENERATE TOPOLOGY (also make sure that SEQUENCE entry does not exist in the alignment or that
no alignment is in memory).
Example:
# Example for: ROTATE_DIHEDRALS