Remodel in Pyrosetta

The Rosetta binary Remodel is a great tool as it allows interesting designs to be made. However, it is rather incompatible with Rosetta Scripts and Pyrosetta as it is heavily dependent on command line options for customisation and repeats some of the processes internally. Despite this, it can be cohersed rather effectively to work in Pyrosetta with some convenience and this is how.

Multiple poses in NGLView

As mentioned previously, most of my Pyrosetta operations are done in a Jupyter notebook run in a cluster node. As a result, I am heavily dependent on NGLView, an IPython widget that uses NGL.js. This is nice for some quick tasks, although admitted more limited than the PyMOL mover, which however requires another ssh to forward another port. My Michelanglo webapp uses NGL.js, so I cannot but say good things of NGL.js. However, one or two things in the Python module NGLView are not immediately clear, so I'll quickly cover dealing with multiple poses here.

Things I wish I had known about Raspberry Pis

Raspberry Pis are very fun to play with and are relatively cheap —I believe I have 6 or 7 Pis running across the house. However, very often I learnt a thing or two that I wish I had known beforehand —sometimes rather fortuitously. So here is my list of top "in-hindsight" tips from the perspective of a seasoned coder with no prior electronics experience.

From cartoon to interactive infographic –the sane way

Making cartoon representations (technically vector graphics) in Adobe Illustrator is very fun, whereas the very idea of making a cartoon representation via line plots with Excel, Matlab, R, Plotly etc. would make anyone insane even just thinking about it. Luckily Illustrator images can be coloured based on numerical data in an automated way... without being manually plotted in Excel. Here I discuss exporting the vector graphic and modifying it with D3.js in a Jupyter notebook.

Shake it like a polaroid picture: MD in pyrosetta

> This blog post has been unfinished for two years. So I am posting in the hopes it will spur me to finish it.

The score of a pose reflects how good its interactions are in that static arrangement, a static snapshot. However, given some energy several of these interactions may break and a different conformation is seen. The best way to describe what does 1 kcal/mol mean is that it is the typical strength of a hydrogen bond, but this is rather weak... in fact this is also the average collision energy of water molecules at 37°C, because that is the molar Boltzmann constant times temperature (k_BT/N_A). (At that point in the explanation is it paramount to resist the urge to explain that k_BT coincides with the mean of the Boltzmann distribution describing the energy of collisions as per Maxwell–Boltzmann statistics or else you get that glazed look thermodynamics seems to illicit even in folk that aren't hangover students)

Therefore, hydrogen bonds do come apart and together rather frequently and in some cases these dynamic properties result large scale switching. This cannot really be determined from a static score —even the per residue scores aren't an indication of dynamic properties. So how does one do an MD run in Pyrosetta?

Remote notebooks and Jupyter themes

Jupyter notebooks are great. PyCharm is great for writing a module, but Jupyter notebook let's you test snippets of code really easily. You can add a Julia kernel, run bash and JS snippets and add markdown notes. The even greater thing is that you can run them off remote machines. If you have too many notebooks on different machines it gets confusing, but luckily there is jupyter themes that let's you customise the colours. Here are the different colours.

XML to Pyrosetta: EvolutionaryDynamicsMover as an example

In the previous post I discuss the strategies to use a Pyrosetta class when the documentation lets you down. One topic discussed was the conversion of a Rosetta XML script to Pyrosetta. Here is an example, namely using the EvolutionaryDynamics mover as an example.