Tuesday 19 February 2019

Uniprot XML and Python ElementTree

Biopython does not have support for Uniprot. The reason is because it holds so much data that it would defeat the point to introduce a complex standard that the user would have to try and remember and the best way is for the user to choose themselves what piece of data they want.
Here I discuss the best way to deal with Uniprot XML files using ElementTree, which is really nice, but awkward at times, hence why I talk about a few monkeypatches that help. If you do not wish to deal with ElementTree (say you want a really quick, bu messy fix) see my post about complicated dictionaries.

Tuesday 5 February 2019

PDB in Office 365

Today I noticed that Word and the rest of Office 365 (i.e. Powerpoint included) can read .obj files (Wavefront files).
This means that I can export in PyMol (via the command "save whatever.obj") a .pse/.pdb to .obj file and open it in Word or Powerpoint or even Outlook. Quite fun and potentially useful little feature. Do note that colours are obviously lost, so it is a bit limiting. The loss of colour is due to PyMOL (Blender exported Wavefront files are textured). Also, only the cartoon of every residue is given, not only visible, and all sticks etc. are lost.