6. Selection exporters

The classes in this module allow writing a selection to a file that can be read by another programme to select the atoms in a MDAnalysis MDAnalysis.core.AtomGroup.AtomGroup. Such cross-package interoperability allows a user to combine their favourite tools with MDAnalysis for further visualization or simulation.

There exist different SelectionWriter classes for different package. The get_writer() function can automatically pick the appropriate one, based on the file name extension in the table below.

Table of supported exporters and recognized file name extensions.
Name extension IO remarks
vmd tcl w VMD macros, available in Representations; module MDAnalysis.selections.vmd
pymol pml w simple PyMOL selection string; module MDAnalysis.selections.pymol
gromacs ndx w Gromacs index file; module MDAnalysis.selections.gromacs
charmm str w CHARMM selection of individual atoms; module MDAnalysis.selections.charmm
jmol spt w Jmol selection commands; module MDAnalysis.selections.jmol