Wrap to MIC#

Wrapping atomic coordinates into the Minimum Image Convention (MIC) box.

The function molsysmt.pbc.wrap_to_mic() folds coordinates into the minimum image convention centered on a reference selection (such as a solute macromolecule).

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.pbc.wrap_to_mic().

Basic usage#

Let’s wrap a solvated peptide system into the minimum image convention centered on the peptide solute:

import molsysmt as msm

molsys = msm.convert(msm.systems['Met-enkephalin']['met_enkephalin.h5msm'])
molsys_solvated = msm.build.solvate(molsys, box_shape='truncated octahedral', clearance='14.0 angstroms', engine='PDBFixer')

Note

Demo Systems Catalog

This tutorial uses demonstration datasets provided by MolSysMT. To explore the full catalog of bundled systems, forms, and file paths, visit the Demo Systems guide.

We wrap the solvent coordinates to the minimum image convention around the peptide while preserving covalent bonds:

molsys_mic = msm.pbc.wrap_to_mic(
    molsys_solvated,
    center_of_selection='molecule_type=="peptide"',
    compact='component'
)

We visualize the wrapped solvated system in 3D using MolSysViewer:

msm.view(molsys_mic)