Documentation of PyMOL-PUB

Structural bioinformatics is a vital field within bioinformatics, focused on the analysis and prediction of the 3-dimensional structure of biological molecules, including proteins, RNA, and DNA. As a key bridge between structural biology and bioinformatics, structural visualization tools play a crucial role in advancing the field by providing visualization of structural information. The current process of creating publication-quality figures can be time-consuming for structural biologists, as no useful tool is currently available for generating figures directly from structure data. Therefore, the integration of end-to-end visual interfaces becomes a pressing necessity.

We have developed an open-source tool of PyMOL framework, named PyMOL-PUB, to streamline the creation of publication-quality figures from molecular structure data. This extension offers a range of features, including structural alignment methods, functional coloring schemes, conformation adjustments, and layout plotting strategies. These functions enable users to easily and rapidly generate publication-quality figures that highlight structural differences (or variations), showcase the connections between physicochemical properties and molecular structures, and/or illustrate inter-molecular interactions.

To summarize, we believe that PyMOL-PUB provides users with a flexible platform to efficiently construct high-resolution figures for customized visualization, driving the rapid advancement of structural biology.