Development & Implementation of a PyMOL 'putty' Representation

PyMOL (http://pymol.org) is an open-source software package designed for molecular graphics visualization and modelling. The PyMOL code-base is written in the C programming language, and much of the higher-level, useraccessible functionality is coded in Python. This software engineering design endows PyMOL with a rich Python application programming interface (API), which end-users can utilize for achieving non-trivial tasks such as loading and analyzing MD trajectories, parsing and analyzing virus structures, and so on. In short, PyMOL is highly extensible. My motivation for introducing ‘sausage’–style cartoons stemmed from a desire to represent arbitrary molecular properties in a cartoon format, such that the diameter of the tubular spline that traces the backbone of the biopolymer would vary proportionately with some property of interest (as encoded in the B-factor field of the PDB file). The only other molecular graphics program which I am aware of as being able to render variable-width cartoons is the MOLMOL software from the Wüthrich lab (ETH-Zürich); in that case, the MolVis software is typically used to represent, say, the position-specific RMSD in a bundle of NMR structures. In the case of MD simulations, one may wish to use such a representation style to visualize and display the coordinate root-mean-square fluctuation (RMSF) along a dynamics trajectory. Also, inclusion of ‘sausage’-style graphical representations has been on PyMOL’s ToDo list for some time (personal communication, WL DeLano).