Monday 22 January 2024

Custom carbon colours in py3Dmol

 Due to NGLView (the Python module) having a frozen older IPywidget version it breaks Colab and the major change for the latter library was a year ago (early 2023), so I am forced to revisit old code and switch to py3Dmol in my Colab demos. Today I figured out how to use custom carbon colours.

Sunday 31 December 2023

A possible BioB bipass route

Nearly a decade ago there was something bugging me and I believe I have figured it out —although it's pointless now. Namely, is another way of making biotin possible without using BioB, biotin synthase, an incredibly slow multistep radical SAM enzyme. 

Thursday 24 August 2023

Reading compressed molecular files on NFS


There are some tasks that make one feel like a failed door-to-door evangelist, one amongst these is proselyting about using compressed files on networked file systems. Namely, NFS are slower than local SSD drives, so most often it is actually quicker to read compressed files in memory rather than decompress them to disk. Here are two Python snippets for dealing with small molecule files.

Sunday 2 July 2023

A note on PLIP interactions

PLIP is a handy tool to enumerate the interactions of a given ligand. However, a few of tripping point I keep having is related to the fact the interactions are namedtuples. Here are some notes to circumvent the traps.

Sunday 5 March 2023

7 colour electronic paper

For Christmas I recieved a 5.65" seven-colour e-paper display, which is awesome. The catch as everything with a Raspberry Pi or Arduino is that beyond the gloss of the advert is something that is far from a flexible plug and play system. I enjoyed my voyage, but it was rather odd even if typical of a Raspberry Pi project.

Saturday 18 February 2023

Swapped university logo colour generator

Like many in academia I have moved across a few universities, each with their own colours, blue, gold, grey (I think) and even pine green (yes, like John Deer merch). Universities are quite possessive of their logos and have guidelines on their 'brand identity', which feels alien to academia as we are used to logos for tools being made in PowerPoint if they even have one. One thing that is frowned upon is changing the colours. But the fondness for ones former and present affiliations should not stand in the way. Luckily I have written a JS tool to help you swap the colours!

Sunday 5 February 2023

Reading a mmCIF from PyMOL in PyRosetta

The mmCIF (PDBx as in extended PDB) format is meant to replace PDB format. Soon the RCSB PDB will have to adopt 4-letter codes for novel chemical components, which will break the PDB format. PDBx format is space separate as opposed to the really annoying column position in the PDB format and in the PDBx format the metadata can be stored in a nearly sensible manner. However, PDBx is solely a deposition format, but it is not really used as analysis format regardless of what the PDB claims. I personally had to add support for it because a reviewer asked me to. This lack of adoption is often attributed to the "if it ain't broken don't fix it" principle. Although I personally would argue that it may due to how it's implemented: opening a PDBx from one program ought to work in another, but this is not often the case. An example of this is PyMOL files read in PyRosetta.