MDAnalysis selects atoms from the PBC box but does not shift the coordinates

Question

MDAnalysis distance selection commands like 'around' and 'sphzere' selects atoms from periodic image (I am using a rectangular box).

universe.select_atoms("name OW and around 4 (resid 20 and name O2)")

However, the coordinates of the atoms from the PBC box reside on the other side of the box. In other words, I have to manually translate the atoms to ensure that they actually are withing the 4 Angstrom distance.

Is there a selection feature to achieve this using the select_atoms function?

Answer 1

If I well understand, you would like to get the atoms around a given selection in the image that is the closest to that selection.

universe.select_atoms does not modify the coordinates, and I am not aware of a function that gives you what you want. The following function could work for an orthorhombic box like yours:

def pack_around(atom_group, center):
    """
    Translate atoms to their periodic image the closest to a given point.

    The function assumes that the center is in the main periodic image.
    """
    # Get the box for the current frame
    box = atom_group.universe.dimensions
    # The next steps assume that all the atoms are in the same
    # periodic image, so let's make sure it is the case
    atom_group.pack_into_box()
    # AtomGroup.positions is a property rather than a simple attribute.
    # It does not always propagate changes very well so let's work with
    # a copy of the coordinates for now.
    positions = atom_group.positions.copy()
    # Identify the *coordinates* to translate.
    sub = positions - center
    culprits = numpy.where(numpy.sqrt(sub**2) > box[:3] / 2)
    # Actually translate the coordinates.
    positions[culprits] -= (u.dimensions[culprits[1]]
                            * numpy.sign(sub[culprits]))
    # Propagate the new coordinates.
    atom_group.positions = positions

Using that function, I got the expected behavior on one of MDAnalysis test files. You need MDAnalysisTests to be installed to run the following piece of code:

import numpy
import MDAnalysis as mda
from MDAnalysisTests.datafiles import PDB_sub_sol

u = mda.Universe(PDB_sub_sol)
selection = u.select_atoms('around 15 resid 32')
center = u.select_atoms('resid 32').center_of_mass()

# Save the initial file for latter comparison
u.atoms.write('original.pdb')
selection.write('selection_original.pdb')

# Translate the coordinates
pack_around(selection, center)

# Save the new coordinates
u.atoms.write('modified.pdb')
selection.write('selection_modified.pdb')