CellPACK: Programs for Creating and Visualizing 3D Models of Cellular Environments
The CellPACK suite of programs are designed to create and visualize 3D models of cellular environments. This initiative builds on illustrative work from the Goodsell laboratory, and foundational methods were developed by Graham Johnson and Ludovic Autin during Johnson’s graduate work in the Olson laboratory.
Programs in the CellPACK suite are currently under active development, so please expect a steep learning curve for many of them. We are currently working to produce tutorials and documentation.
CellPACK is being developed and maintained with support from the US National Institutes of Health.
Structural Model of a Whole Mycoplasma Cell
Movie by Martina Maritan, based on Journal of Molecular Biology 434 (2022) 167351
CellPACK
CellPACK generates 3D models of cells based on a recipe of membranes, membrane-bound proteins, and soluble molecules. A tutorial for it is available at https://www.autopack.org/tutorials/nbcr-summer-training-2018. It is built on AutoPACK, a general tool for packing differently-shaped objects into a given space, which is available at http://autopack.org.
CellVIEW
CellVIEW is a new tool that provides fast rendering of very large biological macromolecular scenes and is inspired by state-of-the-art computer graphics techniques. CellVIEW is implemented in a free-to-use game engine, unity3D. CellVIEW provides fast rendering by introducing new means to efficiently reduce the amount of processed geometries. CellVIEW is unique and has been specifically designed to match the ambitions of structural biologist to model and interactively visualize structures comprised of several billions atoms, such as this model of an entire HIV virion in blood plasma. CellVIEW was created in collaboration with Mathieu Le Muzic and Ivan Viola from the Vienna University of Technology. The software is free for download at http://www.autopack.org/home/cellview
CellPAINT
CellPAINT is a program for creating mesoscale illustrations of HIV, blood serum, and T-cells based on experimental molecular structures. Using the program, you can draw membranes and add molecules to build up a custom scene. It is available at http://ccsb.scripps.edu/cellpaint
Mesoscope
Mesoscope is an interactive web-based tool for generation and curation of mesoscale recipes.
Lattice Nucleoids
LatticeNucleoid tools are used to generate models of viral and bacterial nucleoids.