Friday, 20 June 2014

Week 2 Many plots!

This week I have managed to make a Ramachandran plot for ILE using the top500 pdb files. It seems like the majority of the ILE phi psi angles fall in the beta-sheet and alpha-helix regions with very few in the left hand alpha-helix region. This was expected as the left hand alpha-helix is much rarer.

Following this I also made plots of the chi 1 and chi 2 angles according to their secondary structure. This gave some interesting results showing that in alpha helix the  x1 tended be in distinct regions. There was also some interesting results as when the back bone was in the beta sheet conformation there was a population in the chi 2 in +100.

This is just one of the 4 plots! also made the for ILE residers depending on the backbone conformation.

(disclaimer the figure is not finished yet!)

Based on these plots I have taken a selection of angle combination for phi, psi, chi 1 and chi2 and generated the structures. I hope to be able to optimise them soon but it seems I still have trouble with writing the input files for Gaussian 09. Oh well at least I understand for loops in python better!


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