All Actions are controlled by key-value pairs that specify all tunable parameters, such as action duration, transition smoothness or color of the highlight. overlap only partially with one another): following the above example, it is possible to start the rotation when the zoom-in and animation are already underway. Moreover, Actions can be asynchronous (i.e. one can rotate the view while simultaneously zooming in and animating the trajectory. In Molywood, many Actions can overlap in time, e.g. Most movies will consist of a single Scene, so here we focus on Actions first.Īn Action is the main primitive that abstracts a single event-a rotation, zoom, highlight, etc.-either with a specific duration or effected instantaneously. A Script is a collection of Scenes, and defines the entire movie similarly, a Scene is a collection of Actions and can be thought of as a single panel. Molywood is organized around three hierarchical concepts: Scripts, Scenes and Actions (Fig. Finally, we provide a library of minimal working examples and featured full-fledged movies-hosted at /molywood-to guide users through the supported options. With an easy-to-follow syntax and flexible composition rules, the tool greatly simplifies movie design, allowing the user to focus on conceptual rather than technical issues. These shortcomings prompted us to create Molywood, a Python tool capable of managing complex moviemaking workflows across a range of utilities, including the open-source utilities FFmpeg and Imagemagick, Python’s Matplotlib and VMD with its extended Tcl scripting capabilities ( Humphrey et al., 1996). While molecular movies of excellent quality do exist in the literature, they are usually a result of a lengthy work on integrating workflows, automatizing and post-processing. Simultaneously, platforms such as Molecular Maya are commercial and thus not accessible to many researchers. In fact, a very limited choice of such tools exists today: VMD’s Movie Maker remains limited to simplest cases, BioBlender and ePMV require programming and/or Blender skills ( Andrei et al., 2012 Johnson et al., 2011), while PyMOL’s eMovie effectively vanished from the Web ( Hodis et al., 2007 Hsin et al., 2008). On the other hand, researchers often find existing tools inadequately suited to these challenges. Not only are publishers starting to actively encourage the use of multimedia in the new enhanced, web-only article formats, but also science communication has become increasingly visual due to the proliferation of science-oriented blogs, vlogs and social media channels ( Welbourne and Grant, 2016). This situation could be rectified through widespread adoption of molecular movies as a complementary visual aid in the dissemination of scientific findings ( McGill, 2008). However, the scientific communication of these findings primarily relies on still images and figures, often obscuring or distorting the structural insights. The two revolutions in high-resolution structural biology-first in X-ray crystallography, second in cryogenic electron microscopy (cryo-EM) imaging ( Stuart et al., 2016)-resulted in tens of thousands of unique protein structures being deposited in public databases, ultimately providing us with an atomistic-level insight into the peculiar world of molecular shapes and conformational changes. Since the groundbreaking resolution of the 3-dimensional structure of myoglobin in 1960 ( Kendrew et al., 1960), our understanding of processes of life has increasingly relied on the visualization of molecules.
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