PICK_RESTRAINTS -- pick restraints for selected atoms

RESIDUE_SPAN_RANGE = <integer:2>	0 99999	range of residues spanning the allowed distances; for MAKE_RESTRAINTS, PICK_RESTRAINTS, non-bonded dynamic pairs
RESTRAINTS_FILTER = <real:35>	999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999 999	keep restraints?
RESTRAINT_SEL_ATOMS = <integer:1>	1	a restraint other than non-bonded pair has to have at least as many selected atoms
ADD_RESTRAINTS = <logical:1>	off	whether to add new restraints to existing restraints

Description:

This command selects some or all of the restraints currently in memory.

If ADD_RESTRAINTS is on, the already selected restraints remain selected; additional restraints also become selected if they satisfy currently specified conditions (see below). If ADD_RESTRAINTS is off, only those restraints that satisfy currently specified conditions become selected. This command runs over all restraints in memory, including the currently unselected restraints. Be careful about this: If you have some unselected restraints in memory, PICK_RESTRAINTS may select them; to prevent this, do CONDENSE_RESTRAINTS before calling PICK_RESTRAINTS.

A static restraint is selected if all or at least RESTRAINT_SEL_ATOMS of its atoms are selected (set 1), if it is strong enough based on its standard deviations or force constants (see the next paragraph), and if it does not span less (more) than the minimal (maximal) allowed number of residues specified by RESIDUE_RANGE. Note that here the RESTRAINT_SEL_ATOMS is used also for the static non-bonded restraints, while MAKE_RESTRAINTS and OPTIMIZE commands use NONBONDED_SEL_ATOMS for this purpose (RESTRAINT_SEL_ATOMS is used in MAKE_RESTRAINTS only for most restraint type other than non-bonded pairs).

To decide if a restraint is strong enough, the current standard deviations or force constants are compared with the corresponding RESTRAINTS_FILTER[physical_restraint_type]. A harmonic restraint, lower and upper bounds, and multi-modal Gaussian restraints are selected if the (smallest) standard deviation is less than the corresponding RESTRAINTS_FILTER[i]. The cosine energy term is selected if its force constant is larger than the corresponding RESTRAINTS_FILTER[i]. If RESTRAINTS_FILTER[i] = $-999$, a restraint of type $i$ is always selected. Restraints of the other physical_restraint_types are always selected (Coulomb, Lennard-Jones, binormal, and spline). The RESTRAINTS_FILTER angles have to be specified in radians.

Example:

# Example for: PICK_RESTRAINTS, CONDENSE_RESTRAINTS

# This will pick only restraints that include at least one
# CA atom and write them to a file.

SET OUTPUT_CONTROL = 1 1 1 1 1

READ_TOPOLOGY   FILE = '$(LIB)/top_heav.lib'
READ_PARAMETERS FILE = '$(LIB)/par.lib'
READ_MODEL FILE = '1fas'
SEQUENCE_TO_ALI ATOM_FILES = '1fas', ALIGN_CODES = '1fas'
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES '1fas.ini', ;
                ALIGN_CODES = ALIGN_CODES '1fas-ini'
GENERATE_TOPOLOGY SEQUENCE = '1fas-ini'
TRANSFER_XYZ
BUILD_MODEL INITIALIZE_XYZ = off

MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo'
ENERGY

PICK_ATOMS ATOM_TYPES = 'CA N C O'
PICK_RESTRAINTS ADD_RESTRAINTS = off, RESTRAINT_SEL_ATOMS = 1
# Delete the unselected restraints from memory:
CONDENSE_RESTRAINTS
ENERGY

WRITE_RESTRAINTS FILE = '1fas.rsr'