Summary Computing a PNG image for each of 1,000 PDB files 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 (GUI.) However, there are situations where it may be beneficial to run PyMOL without using the mouse. I recently computed …
UW personnel has access to Box, a cloud drive to store documents. While the older “Box Sync” application kept a copy of every file and folder on the local computer, the newer “box drive” software keeps only chosen folders or files on the local machine, everything else stays in the “cloud.” The location of …
Sometimes a very simple command can accomplish amazing tasks. Recently I had a list with alternating entries on every other line with about 200 lines, and lots of uneven text. But I wanted to have 2 columns instead. A quick online search let me find a new way of using a familiar command called …
…provides a wonderfully well done, easy to understand set of small tutorials, with exercises, each with an accompanying video that should make it easier for beginners that want to learn Unix command line / bash…. To make is faster to navigate the lessons and videos I have combined both into a simple table…
In some instances we start a container, but it will default to immediately running a program within and prevent immediate shell access. This is possible since Docker version1.3 Assuming that the container is already running (for example serving a web browser) and you can’t access the shell commands we can gain shell (bash, ssh) through …
When activated by the docker run command, some docker container immediately start a software within. This can be useful for the author of the image, but for others it may cause issues. Here is one example amongst many, from a series: Bioinformatics Docker Images Project which may be difficult for some users due to the use of …