Summary We run a script to compute the distance between 2 atoms in a series of PDB files with identical molecules in different conformations and save the distance results into a plain text file. No …
Docker
Python NumPy 2.0 incompatibilities
Summary The new Numpy 2.0 is not compatible with many other packages, as I discovered after many lost hours. The final Docker images can be downloaded from alleleanalyzer. NumPy in a Docker I was interested …
New Tutorial Section: Computational Modeling
Computational Modeling This is the general title of a new Tutorials pull-down menu that will be populated with new or updated tutorials. It can be found within the Tutorials menu list as Computational Modeling The …
Rosetta Ligand Docking – Help with Docker
Summary Combine software and scripts on Docker and local macOS computer (Intel amd64 or arm64 Silicon Chip M series) to follow successfully the Rosetta tutorial Ligand Docking with a G-Protein Coupled Receptor. This method will …
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 …
Install Local Docker Desktop on macOS without Admin
Summary Instructions to install Docker on macOS for which user does not have Admin privileges. These instructions are meant for iMacs in Biochem 201 but should work on any Mac. Procedure Download Docker Desktop from …
Interactive bioinformatics tutorials
Summary sandbox.bio provides interactive tutorials for exploring bioinformatics command-line tools within a web browser. Bioinformatics When people ask “what is bioinformatics” I have to pause. When I named a computer “bioinformatics” at the dawn of …
AlphaFold2 with full databases and multimer option
Summary This article describes running AlphaFold2 with full databases at the UW-Madison Center for High Throughput Computing (CHTC) and is part of an article series titled Five ways to run AlphaFold. CHTC cluster, HTCondor, Containerization …
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 …
Using Docker containers on Biochemistry Linux Cluster
Summary A short example on running software within a Docker container on a Linux cluster. Since the software is installed within the container no installation is necessary. The computation can be scaled to accommodate large …