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.

Tuesday, 15 January 2019

Phosphorylated PDB files

Sometime in human protein, a residue is phosphorylated, yet the model one gets from I-TASSER, Phyre etc. or the actual PDB structure lacks these. Here is how to add them easily and quickly with Rosetta.

Wednesday, 19 December 2018

A failsafe decorator for a python class

Often a Python class may have lots of bound methods that may fail, but it is not really a problem. Here I present a tidy way to deal with catching the errors with a decorator.

How to deal with horrid XML dictionaries in Python

NCBI and Uniprot data is stored as byzantine XMLs, which have rather consistent schema, but hard to decipher. You can spend ages trying to find the series of keys and indices required to find a given value.
Here I present a nice pair of Python methods to get a given key or value in a convoluted object of nested dictionary-like and list-like objects.

Tuesday, 18 September 2018

Python website on a shoestring budget, a tutorial

If you have a Python script you want to make into a website yet want to do it for a cheap as possible, it may seem like an impossible cause. But it isn't. Three options are possible:
  1. use a free service
  2. use a grant-based service
  3. run a server at home on a Raspberry Pi
Each have their merits, but the latter more so. Hence, why this tutorial is dedicated to showing you how to do it.

Everything you wanted to know about isopeptide bonds in Rosetta, but were too afraid to ask

Rosetta is great at predicting (with some accuracy) the energies of variant proteins, however, to make the most out of it with proteins with internal isopeptide bonds a few considerations are needed.

Saturday, 25 August 2018

PCR distribution

The distribution of mutations in an error prone library has been modelled in Sun (1995) based on the underlying principle of a PCR reaction. In the paper it is found that the distribution becomes more and more similar to a regular Possion and the two are virtually the same after 10 cycles. However, given that one most likely does not know what one's PCR efficiency is, using this formula may be dangerous. Whereas in reality getting a better estimate of the mean number of mutations may be more helpful.