BlendMolBlendMol is a Blender plugin that can easily import VMD ‘Visualization State’ and PyMOL ‘Session’ files. BlendMol empowers scientific researchers and artists by marrying molecular visualization and industry-standard rendering techniques. The plugin works seamlessly with popular analysis programs (i.e., VMD/PyMOL). Users can import into Blender the very molecular representations they set up in VMD/PyMOL.
Dimorphite-DLDimorphite-DL adds hydrogen atoms to molecular representations, as appropriate for a user-specified pH range. It is a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states.
Gypsum-DLGypsum-DL is a free, open-source program that converts 1D and 2D small-molecule representations (SMILES strings or flat SDF files) into 3D models. It outputs models with alternate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational states.
ProteinVRProteinVR is a web-based application that allows users to view protein/ligand structures in virtual reality (VR) from their mobile, desktop, or VR-headset-based web browsers. Molecular structures are displayed within 3D environments that give useful biological context and allow users to situate themselves in 3D space.
PyritePyrite is a Blender plugin that imports the atomic motions captured by molecular dynamics simulations. Using Pyrite, these motions can be rendered using Blender’s state-of-the-art computer-graphics algorithms. All 3D protein representations (e.g., surface, ribbon, VDW spheres) are supported. Aside from advancing scientific and collaborative objectives, Pyrite renderings will also appeal to students and non-specialists.
ScoriaScoria is a Python package for manipulating three dimensional molecular data. Unlike similar packages, Scoria is written in pure Python and so requires no dependencies or installation. One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. Rather, it complements them. Our package leverages others (e.g., NumPy, SciPy, MDAnalysis), if present, to speed and extend its own functionality.