Specification of pseudo atoms

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.

Gravity center of all of the supplied atoms.

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 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 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 aliphatic proton on a tetrahedral carbon (-$ >$ CH), defined by the central C and the three other substituents (specified by 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 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).

Example: examples/python/pseudo_atoms.py

from modeller import *
from modeller.scripts import complete_pdb
from modeller.optimizers import conjugate_gradients

env = environ()

env.io.atom_files_directory = ['../atom_files']

# 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.gravity_center(allca)

# Constrain every C-alpha to be no more than 10 angstroms from the center
for at in allca:
    r = forms.upper_bound(group=physical.xy_distance,
                          feature=features.distance(at, center),
                          mean=10.0, stdev=0.1)

# Constrain the gravity center to the x=0 plane
r = forms.gaussian(group=physical.xy_distance,
                   mean=0.0, stdev=0.1)

# Keep sensible stereochemistry
rsr.make(allat, restraint_type='stereo', spline_on_site=False)

# Optimize with CG
cg = conjugate_gradients()
cg.optimize(allat, max_iterations=100, output='REPORT')

Automatic builds 2017-07-19