Rapid generation of high-quality structure figures for publication with PyMOL-PUB
Yuting Chen, Haoling Zhang, Wen Wang, Yue Shen, Zhi Ping- Computational Mathematics
- Computational Theory and Mathematics
- Computer Science Applications
- Molecular Biology
- Biochemistry
- Statistics and Probability
Abstract
Motivation
The advancement of structural biology has increased the requirements for researchers to quickly and efficiently visualize molecular structures in silico. Meanwhile, it is also time-consuming for structural biologists to create publication-standard figures, as no useful tools can directly generate figures from structure data. Although manual editing can ensure that figures meet the standards required for publication, it requires a deep understanding of software operations and/or program call commands. Therefore, providing interfaces based on established software instead of manual editing becomes a significant necessity.
Results
We developed PyMOL-PUB, based on the original design of PyMOL, to effectively create publication-quality figures from molecular structure data. It provides functions including structural alignment methods, functional coloring schemes, conformation adjustments, and layout plotting strategies. These functions allow users to easily generate high-quality figures, demonstrate structural differences, illustrate inter-molecular interactions and predict performances of biomacromolecules.
Availability and Implementation
Our tool is publicly available at https://github.com/BGI-SynBio/PyMOL-PUB.
Supplementary information
Supplementary data are available at Bioinformatics online.