POSE: build, manipulate, mutate, L, D, protein molecular structures

Summary Pose is a Python library for building and manipulating protein molecular structures. Builds with L- and D- amino acids or a mixture; can open existing PDB structures. Computes many molecular properties. Pose Library Pose …

3D Protein Imager a PyMOL/Qutemol web alternative

Summary Molecule of the Month In the year 2000 David Goodsell started to provide stories on the The Protein Data Bank web site as the “molecule of the month” with his unique style that was …

Faster image creation in PyMOL: Shortcuts and Docker

Summary PyMOL command scripts are available natively and within Docker images. PyMOL Scripts PyMOL offers a very easy-to-use graphical user interface (GUI) to manipulate loaded molecule, and alter the appearance and coloring options. However, while …

No GUI PyMOL for high throughput images and optional Docker

Summary Computing a PNG image for each of 1,000 PDB file as a cartoon, color-coded by B factor. PyMOL without GUI PyMOL is routinely used by Biologists to illustrate molecules, using the graphical user interface …

AlphaFold2 on Macintosh M1

Summary This post is a summary of installation of AlphaFold2 onto a Macintosh with an M1 style (arm64) computer chip (i.e. not an Intel/AMD Chip.) This post started with the blog post Installing Alphafold2 on …