I recently had a problem where I wanted to provide an interactive visualization of multiple different protein–ligand complexes, requiring minimal setup by the user, allowing them to zoom in and out and change the visualization style, without just providing multiple PDB files or a PyMOL session.
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Open Source PyMOL installation on Windows
A year ago, I used Gheorghe Rotaru’s helpful blog post to install PyMOL. Unfortunately, after resetting my computer, I have just discovered that some of the links are broken. Here are the installation steps with new links provided by Christoph Gohlke, who generously offers pre-compiled Windows versions of the latest PyMOL software along with all its requirements.
Install the latest version of Python 3 for Windows:
Download the Windows Installer (x-bit) for Python 3 from their website, with x being your Windows architecture – 32 or 64.
Follow the instructions provided on how to install Python. You can confirm the installation by running ‘py’ in PowerShell.
Online tools for drawing and visualizing molecules
I recently came across a nice tool for depicting multiple molecules called CDK Depict (thanks to Ruben for sending it to me), so I decided to explore what other web-based molecule visualization and drawing tools are available.
Continue readingTips & tricks with PyMOL
I have been using PyMOL, a molecular visualisation program, throughout my PhD and wanted to share some of the things I’ve learned.
1. Installation
Open source PyMOL can be installed using conda: conda install -c conda-forge pymol-open-source. It does not watermark figures and has full functionality, as far as I have been able to tell.
histo.fyi: A Useful New Database of Peptide:Major Histocompatibility Complex (pMHC) Structures
pMHCs are set to become a major target class in drug discovery; unusual peptide fragments presented by MHC can be used to distinguish infected/cancerous cells from healthy cells more precisely than over-expressed biomarkers. In this blog post, I will highlight a prototype resource: Dr. Chris Thorpe’s new database of pMHC structures, histo.fyi.
histo.fyi provides a one-stop shop for data on (currently) around 1400 pMHC complexes. Similar to our dedicated databases for antibody/nanobody structures (SAbDab) and T-cell receptor (TCR) structures (STCRDab), histo.fyi will scrape the PDB on a weekly basis for any new pMHC data and process these structures in a way that facilitates their analysis.
Continue readingHow to Install Open Source PyMOL on Windows 10
It is possible to get an installer for the crystallographer’s favourite molecular visualization tool for Windows machines, that is if you are willing to pay a fee. Fortunately, Christoph Gohlke has made available free, pre-compiled Windows versions of the latest PyMOL software, along with all of it’s requirements, it’s just not particularly straightforward to install. The PyMOLWiki offers a three-step guide on how to do this and I will break it down to make it somewhat clearer.
1. Install the latest version of Python 3 for Windows
Download the Windows Installer (x-bit) for Python 3 from their website, x being your Windows architecture – 32 or 64.
Then, follow the instructions on how to install it. You can check if it has installed by running the following in PowerShell:
Continue readingMaking 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.
PyMOL: colour by residue
PyMOL is a handy free way of viewing three dimensional protein structures. It allows you to toggle between different representations of the protein – such as cartoon, surface, sticks, etc. – which all have their own pros and cons.
However one thing I felt that PyMOL lacked was an easy way to visually distinguish residues based on type. Whist you can easily differentiate atom types based on colour in the colour menu, and even choose which colour you wish carbons to show up as whilst keeping heteroatoms different colours, this assigned carbon colour would be constant throughout the entire protein.
Using Python in PyMOL
Decades later, we owe Warren DeLano and his commitment to open source a great debt. Warren wrote PyMOL, an amazingly powerful and popular molecular visualization tool, but it has many hidden talents.
Perhaps its greatest strength is the use of the open source language, Python, as its control language.
Continue readingPyMOL: colouring proteins by property
We all love pretty, colourful pictures of proteins. There is quite a variety of programs to produce publication-quality images of proteins, some of the most popular being VMD, PyMOL and Chimera. Each has advantages and disadvantages — for example, VMD is particularly good to deal with molecular dynamics simulations (perhaps that’s why it is called “Visual Molecular Dynamics”?), and Chimera is able to produce breathtaking graphics with very little user input. In my work, however, I tend to peruse PyMOL: a Python interface is incredibly helpful to produce quick analyses.
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