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Exploration of Electron Density and Cryo-EM Potential

in ultra-high resolution protein structures
and a geometric analysis for criteria searching of density areas of interest

The primary purpose of my PhD is to look for new information about interatomic bonds from ultra-high resolution x-ray crystallographic maps. The explosion in the solutions of ultra-high resolution structures has led to information about protein crystal structures being sampled up to every 0.3Å in ultra-high structures. With the distances in the peptide bond between atoms being around 1.45Å (Engh&Huber, 2006) this is an opportunity to analyse data sampled within atomic bonds for new informaiton.

The density in a peptide bond

An example of an image of some electron density, where the red is a stronger density.
This is a peptide bond with the C in the middle, the peptide bond to N+1 mid left, the O on the right.

image info

Status notes

29/12/24

  • I have done more than expected and re-implemeted critical point analysis as a new derivative called criticalpoint that categorises a critical point based on the signs of the 2nd partial derivatives as per Bader (1994).
  • All not complete pages I asterisked at the end* but didn't want to remove because they guide me.

25/12/24

This is under development to write up my current progress, nothing is complete currently it is all notes to self.