I wanted to show membrane protein topology in 3-dimensional form with membrane intact. I wanted to show extracellular region, membrane region and intracellular region of protein in 3-d form. I have been using protter but it shows in 2D form only.
For displaying membrane protein topology in three dimensions, open-source tools such as PyMOL, Chimaera, PymolMembrane, MembranePy, MDAnalysis, VMD, and ProLego are available. A well-liked programme for molecular visualisation, PyMOL has a number of plugins and tools for working with protein structures, including membrane proteins. Another tool is Chimaera, and PymolMembrane is a PyMOL plugin made especially for this use. A Python module called MembranePy gives users access to a variety of visualisation tools for producing 3D visualisations. A Python package for molecular dynamics simulations is called MDAnalysis. ProLego is an online platform where users can upload protein structures, while VMD is a tool for molecular visualisation.