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    • BlendMol
      BlendMol 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.
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    • 3 weeks, 4 days ago

       Brady

    • Dimorphite-DL
      Dimorphite-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.
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       Jacob Durrant

    • Gypsum-DL
      Gypsum-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.
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    • PCAViz
      PCAViz is an open-source Python/JavaScript toolkit for sharing and visualizing MD trajectories via a web browser.
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    • Pyrite
      Pyrite 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.
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       Jacob Durrant

    • Scoria
      Scoria 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.
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       Jacob Durrant