GARNISH allows a coarse grained structure to be visualized in pymol like an atomistic structure by drawing bonds and elastic network.

Lysozyme 2VB1 from left to right: crystal structure in cartoon representation, licorice representation with backbone bonds drawn, elastic network visualized using line representation.

pip install git+git://github.com/mjtadema/garnish.git#egg=garnish

To access the function, in PyMOL do import garnish.

garnish [file [, selection [, gmx]]]

• file = a tpr or topology file to extract bond information from (default: None)
• selection = any selection to act upon (default: all)
• gmx = gmx executable path (default: inferred by which gmx)

Without a top/tpr file, this function only adds bonds between the backbone beads so they can be nicely visualized using line or stick representation. Adding a top/tpr file provides topology information that can be used to draw side chain and elastic bonds.

To nicely show your martini system in pymol:

garnish topol.top