There are virtual and pseudo atoms. A virtual atom is an atom that occurs in the actual molecule, but whose position is not represented explicitly in the MODEL and topology file. A pseudo atom is a position that does not correspond to an actual atom in a molecule, but is some sort of an average of positions of real atoms. Pseudo atoms can be added to the list of restraints by adding the objects below to the Restraints.pseudo_atoms list. Atom ids are as for features, above. The MODELLER pseudo and virtual atom types follow closely the GROMOS definitions.
pseudo_atom.GravityCenter(*atom_ids)
Gravity center of all of the supplied atoms.
pseudo_atom.CH2(*atom_ids)
Pseudo aliphatic proton on a tetrahedral carbon (CH2). Not assigned
stereospecifically; its position is between the two real protons; defined by
the central C and the other two substituents (specified by atom_ids).
pseudo_atom.CH31(*atom_ids)
Pseudo aliphatic proton on a tetrahedral carbon (-CH3), defined by the central
C and the heavy atom X in X-CH3 (specified by atom_ids); its position is
the average of the three real protons.
pseudo_atom.CH32(*atom_ids)
Pseudo aliphatic proton between two unassigned -CH3 groups; defined by X in CH3 - X - CH3 and the two C atoms from the two CH3 groups (specified by
atom_ids). Its position is the average of the six real protons.
virtual_atom.CH1(*atom_ids)
Virtual aliphatic proton on a tetrahedral carbon (-CH), defined by the
central C and the three other substituents (specified by atom_ids).
virtual_atom.CH1A(*atom_ids)
Virtual aromatic proton on a trigonal carbon (=CH), defined by the central C
and the two C atoms bonded to the central C (specified by atom_ids).
virtual_atom.CH2(*atom_ids)
Virtual aliphatic proton on a tetrahedral carbon (CH2) assigned
stereospecifically; defined by the central tetrahedral atom and the other two
substituents on it (specified by atom_ids).
from modeller import * from modeller.scripts import complete_pdb from modeller.optimizers import ConjugateGradients env = Environ() env.io.atom_files_directory = ['../atom_files'] log.verbose() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') # Read in the model mdl = complete_pdb(env, "1fdn") rsr = mdl.restraints # Select all C-alpha atoms allat = Selection(mdl) allca = allat.only_atom_types('CA') # Create a pseudo atom that is the center of all C-alphas, and activate it center = pseudo_atom.GravityCenter(allca) rsr.pseudo_atoms.append(center) # Constrain every C-alpha to be no more than 10 angstroms from the center for at in allca: r = forms.UpperBound(group=physical.xy_distance, feature=features.Distance(at, center), mean=10.0, stdev=0.1) rsr.add(r) # Constrain the gravity center to the x=0 plane r = forms.Gaussian(group=physical.xy_distance, feature=features.XCoordinate(center), mean=0.0, stdev=0.1) rsr.add(r) # Keep sensible stereochemistry rsr.make(allat, restraint_type='stereo', spline_on_site=False) # Optimize with CG cg = ConjugateGradients() cg.optimize(allat, max_iterations=100, output='REPORT') mdl.write(file='1fas.ini')