Simon Cross, Michelle M. Kuttell, John E. Stone, and James E. Gain.
Visualization of cyclic and multi-branched molecules with VMD.
Journal of Molecular Graphics and Modelling, 28:131-139, 2009.
(NIHMS: 215013)
CROS2009-JS
We report the addition of two visualisation algorithms, termed PaperChain and Twister, to
the freely available Visual Molecular Dynamics (VMD) package. These algorithms produce
visualisations of complex cyclic molecules and multi-branched polysaccharides and are a
generalization and optimization of those we previously developed in a standalone package
for carbohydrates. PaperChain highlights each ring in a molecular structure with a
polygon, which is coloured according to the ring pucker. Twister traces glycosidic bonds
with a ribbon that twists according to the relative orientation of successive sugar residues.
Combination of these novel algorithms and new ring selection statements with the large set
of visualisations already available in VMD allows for unprecedented flexibility in the level of
detail displayed for glycoconjugate, glycoprotein and carbohydrate-binding protein
structures, as well as other cyclic structures. We highlight the efficacy of these algorithms
with selected illustrative examples, clearly demonstrating the value of the new
visualisations, not only for structure validation, but also for facilitating insights into
molecular structure and mechanism.
