PyMOL and Biological Units from REMARK 350

Summary Compute biological assembly from coordinates with a python script. Symmetry X-ray crystallography solved the mathematical problem to provide 3D (cartesian) coordinates but the resulting “asymmetric unit cell” does not necessarily represent the biological structure. …

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 …

Foundational concepts to understand AI: free online curricula

Summary Alignment Course is an online curriculum that provides materials in a useful order to learn fundamentals. The Governance Course offers similar material at the beginning, but then moves towards governance (regulations etc.). Within the first …

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 …

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 …