title: Simplifying and enhancing the use of PyMOL with horizontal scripts.
abstract: Scripts are used in PyMOL to exert precise control over the appearance of the output and to ease remaking similar images at a later time. We developed horizontal scripts to ease script development. A horizontal script makes a complete scene in PyMOL like a traditional vertical script. The commands in a horizontal script are separated by semicolons. These scripts are edited interactively on the command line with no need for an external text editor. This simpler workflow accelerates script development. In using PyMOL, the illustration of a molecular scene requires an 18-element matrix of view port settings. The default format spans several lines and is laborious to manually reformat for one line. This default format prevents the fast assembly of horizontal scripts that can reproduce a molecular scene. We solved this problem by writing a function that displays the settings on one line in a compact format suitable for horizontal scripts. We also demonstrate the mapping of aliases to horizontal scripts. Many aliases can be defined in a single script file, which can be useful for applying costume molecular representations to any structure. We also redefined horizontal scripts as Python functions to enable the use of the help function to print documentation about an alias to the command history window. We discuss how these methods of using horizontal scripts both simplify and enhance the use of PyMOL in research and education.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma. blaine-mooers@ouhsc.edu.|Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma. blaine-mooers@ouhsc.edu.
authors.forename: Blaine H M
authors.initials: BH
authors.lastname: Mooers
mesh_terms: D012984:Software
keywords: Python scripting; molecular artwork; molecular graphics; molecular literacy; molecular orientation; molecular visualization; reproducible research; scientific communication; scientific illustration