Hi, I have some high quality PDB files I want to extract the torsion angles from to assemble some Ramachandran plots by residue. I understand the PDB file structure and I know how to use the coordinates of the C\alpha/N and C\alpha\C atoms to calculate the angles using dot products, however, I have an issue of wondering how I can parse through all the other atoms in the residues to get the bond angles around C\alpha? Do I have to remove water molecules as well?
I am well versed in Python so any recommendations with that are great but any other pointers would help. Thanks!
Hi Reginald!! You can create a parser that will return only heavy atoms without any problems. You can also use the Biopython PDB library to parse and obtain the coordinates you require. Also, me and my collegues develop a (originally) simple parser that will return an object with all the info you want. In my to do list there is the computation and plotting of the Ramachandran plot, but havent implemented yet. The code can be found in the link below.
Best,
Sergio
https://github.com/LabBlouin/LabBlouinTools/blob/master/labblouin/PDBnet.py
Awesome! Let me review it and if I use it in publication, how should I reference it?
We have not published a note with it, but if you can link our git to your publication we will be grateful!
Cheers!
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