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.
Spilt agar on the keyboard
A sticky mess of disconnected ideas, analyses and just plain silly posts about computational biochemistry, synthetic biology and microbiology.
Monday, 22 February 2021
Sunday, 3 January 2021
Things I wish I had known about Raspberry Pis
Tuesday, 29 December 2020
From cartoon to interactive infographic –the sane way
Sunday, 1 November 2020
Remote notebooks and Jupyter themes
Saturday, 31 October 2020
XML to Pyrosetta: EvolutionaryDynamicsMover as an example
Tuesday, 27 October 2020
Pyrosetta scripting without a manual
I got recently asked how to figure out how to write a Pyrosetta script when there is no example. This is definitely the biggest weakness of Pyrosetta and Rosetta script, but it is not insurmountable. In fact, there is a wealth of information that is hidden that can be mined. Here is how and in the next post, I give an example.
Friday, 9 October 2020
The Freedom unit for molar energy: the foot-pound-force per pound-mole
In computational biochemistry the most commonly used unit is molar energy. The SI unit is kJ/mol (kilojoule per mole), but kcal/mol is also as frequently used —Google enumerates 5.3e6 and 3.8e6 pages for them respectively. Different programs use one or the other, GROMACS uses kJ/mol, while Rosetta uses kcal/mol. They differ by a factor of about 4, the latter has the advantage that 1 kcal/mol is the strength of a hydrogen bond and kBT/NA is 0.6 kcal/mol (25°C) or 1. kcal/mol (37°C), while the former being SI sounds more sciency ——and not in the overly obnoxious way as folk who use Kelvin for enzymology.
However, whereas it is not an SI unit, kcal/mol is still very metric and European, after all the unit calorie was introduced by a Frenchman. Therefore, a more American unit is clearly required. Hence the need for the foot–pound-force per pound-mole.