PyMOL-PUB 1.0

PyMOL-PUB: an extension for publication-quality figure production from structure data

With the rapid progress of fields like protein structure prediction, an increasing number of researchers from different backgrounds require the use of PyMOL for molecular visualization. To be used in publications, the default visualization output of PyMOL typically requires the spatial adjustments, such as rotating and/or zooming the structures, and purposeful emphasis including highlighting important parts and hiding the unimportant parts. Meanwhile, the need for batch visualization has been demonstrated by recent publications in high-impact journals. However, these adjustments and batch protocols require the involvement of many skilled personnel, are expensive, and operate at human speeds, all of which make them worthy of automation. Based on the original design of PyMOL and as an important supplement, we develop a high-level interface in order to generate figures capable of reaching the publication standard. By using our tool, the manual operations can be greatly reduced, and the desired image output can be obtained with a few lines of code or only configuration.