Summary Run the ColabFold version of AlphaFold2 on your laptop (slow without GPU) or on a large Linux cluster. The full tutorial with scripts is located at ColabFold with HTCondor What is AlphaFold2 Excerpt from …
Docker
No GUI PyMOL – computing distances for thousands of PDB files from Rosetta
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 …
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 …
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 …