GARNISH allows a coarse grained structure to be visualized in pymol like an atomistic structure by drawing bonds and elastic network.
The package will be subject to a thorough rewrite in the very near future.
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