Selection.hot_atoms() — atoms violating restraints

hot_atoms(pick_hot_cutoff, residue_span_range=(0, 99999), viol_report_cut=physical.Values(default=4.500000, chi1_dihedral=999.000000, chi2_dihedral=999.000000, chi3_dihedral=999.000000, chi4_dihedral=999.000000, chi5_dihedral=999.000000, phi_psi_dihedral=6.500000, nonbond_spline=999.000000, accessibility=999.000000, density=999.000000, gbsa=999.000000, em_density=999.000000), schedule_scale=None, edat=None)

Output:

Selection

This command evaluates the energy for all atoms in the selection, and returns a new selection containing atoms that should be optimized to remove hot spots in the model; only selected restraints are considered. The scaling factors for the physical restraint types are given by schedule_scale.

More precisely, the command first flags violated selected atoms. An atom is violated if it is part of a violated restraint. A restraint of physical group $x$ (Table 6.1) is violated when its relative heavy violation (see Section 5.3.1) is larger than specified in viol_report_cut[x].

The command then flags those selected atoms that are within the pick_hot_cutoff angstroms of any of the already flagged atoms.

It is often sensible to follow this command with Selection.extend_by_residue(), to select sidechains and neighboring residues.

This command is usually followed by the Restraints.pick() command, to select all the restraints that operate on selected (hot) atoms, and then an optimization (see Section 6.11).

Example: examples/commands/pick_hot_atoms.py

# Example for: Selection.hot_atoms()

# This will pick atoms violated by some restraints (bond length restraints
# here), select restraints operating on violated atoms, and calculate the
# energy for the selected restraints only (note that a list of violated
# restraints can be obtained by the ENERGY command alone).

from modeller import *
from modeller.scripts import complete_pdb

env = Environ()
env.io.atom_files_directory = ['../atom_files']
env.edat.dynamic_sphere = False
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')

# Read the sequence, calculate its topology and coordinates:
mdl = complete_pdb(env, "1fas")

# Just to get some violations:
atmsel = Selection(mdl)
atmsel.randomize_xyz(deviation=0.06)
# Create the bond length restraints and ignore the hard sphere overlap:
mdl.restraints.make(atmsel, restraint_type='bond', spline_on_site=False)
# Pick hot residues and the corresponding violated and neighboring restraints:
atmsel = atmsel.hot_atoms(pick_hot_cutoff=4.0).by_residue()
mdl.restraints.unpick_all()
mdl.restraints.pick(atmsel)
# Calculate the energy of the selected restraints and write them out in detail:
atmsel.energy(output='VERY_LONG')