Category Archives: How To

How to do things. doh.

Making Pretty Pictures with PyMOL

There’s few things I like more in our field than the opportunity to make a really nice image of a protein structure. Don’t judge me, but I’ve been known to spend the occasional evening in front of the TV with a cup of tea and PyMOL open in front of me! I’ve presented on the subject at a couple of our research group retreats, and have wanted to type it up into a blog post for a while – and this is the last opportunity I will have, since I will be leaving in just a few weeks time, after nearly eight years (!) as an OPIGlet. So, here goes – my tips and tricks for making pretty pictures with PyMOL!

Ray Tracing

set ray_trace_mode, number

I always ray trace my images to make them higher quality. It can take a while for large proteins, but it’s always worth it! My favourite setting is 1, but 3 can be fun to make things a bit more cartoon-ish.

You can also improve the quality of the image by increasing the ‘surface_quality’ and ‘cartoon_sampling’ settings.

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BioDataScience101: a fantastic initiative to learn bioinformatics and data science

Last Wednesday, I was fortunate enough to be invited as a guest lecturer to the 3rd BioDataScience101 workshop, an initiative spearheaded by Paolo Marcatili, Professor of Bioinformatics at the Technical University of Denmark (DTU). This session, on amino acid sequence analysis applied to both proteomics and antibody drug discovery, was designed and organised by OPIG’s very own Tobias Olsen.

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Enhance your presentation by using virtual webcams and scene transitions

If you haven’t checked out Matt’s post on using OBS for recording video, I highly recommend doing so. OBS is a terrific way to present your work online. It can provide (amongst many, many other things) the ability to create live picture-in-picture scenes, so you can move through your powerpoint deck whilst overlaying video of your tiny talking head in the corner.

Continuing on from Matt’s post, I’d like to promote the OBS virtual camera plugin and Touch Portal.

Every company, department or course has its own favourite video conferencing application and whilst they all have their strengths, consistency is not one of them. If you want to consistently display your presentation and your live video regardless of the platform in use, this quickly gets into the “messy” territory. This is where the virtual camera comes in.

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Improving your Python code quality using git pre-commit hooks

Intro

I recently completed an internship during which I spent a considerable amount of time doing software engineering. One of my main take-aways from this experience was that in industry, a lot more attention is spent on ensuring that code committed to a GitHub repo is clean and bug-free.

This is achieved through several means like code review (get other people to read your code), test-driven development (make sure your code works as you are adding functionality) or paired development (have two people work together on the same piece of code). Here, I will instead focus on a useful tool that is easy to integrate into your existing git workflow: Pre-commit hooks.

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How to SCP files from a gated server to your personal computer

Jack recently made a blog post in which he provided a script which can transfer your files between your personal computer and a given remote machine via temporarily hosting a file on file.io (blog post here); where you have some sensitive data that you do not want to risk hosting online, you can also fairly easily use SCP to keep business strictly between your local and remote machine.

What I am referring to is described here. This blog post refers to the case where you want to SCP from local host to a remote machine which is only accessible via a gate server (this isn’t necessarily true for the Stats computers as we can use the VPN to directly access our remote machine of choice by the way). I won’t effectively plagiarise the blog post I linked to as the explanation is clear enough in itself, but you just use port forwarding and the localhost address of your local machine!

Best wishes,

Eve

Prerecording Conference Talks and Posters using OBS Studio

Seemingly every conference due to take place this year has either been cancelled or will be run virtually due to the COVID-19 pandemic. Many organisers have decided that running entirely live virtual programmes causes more trouble than it’s worth (e.g. due to unforseeable IT and internet issues disrupting the schedule), and so are asking their presenters to prerecord their talks, which are then broadcast “live” on the day.

I recently “presented” two virtual prerecorded talks at the ISMB conference using Open Broadcast Software Studio (OBS Studio), a free open-source software package most commonly used by live-streamers on Twitch and Youtube. It is super simple to use and achieves a professional output, with video overlaying a presentation slide deck/poster PDF. This blog is a “how-to” on getting started with OBS for conference talks/poster presentations.

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Uploading/downloading small files across systems

Sometimes you just want to quickly move a copy of a script, image or binary from, for example, your local (linux) machine to another (linux) machine. The usual tool would be SCP, but this can get complicated when there are several layers of ssh and sometimes it doesn’t work at all (as is the case for transfers between the Department of Statistics computers and the outside world).

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