I wrote a C program to produce cartesian coordinates of a protein molecule, with internal coordinates (bond angles, bond lengths,ramachandran angles as input). I have not included side chains and hydrogen bonds in the codes. Now to check whether the code is working or not, I took crambin protein data from the internet and took the ramachandran angles using VMD and used those angles for my code to check it. Though my code produces two alpha helices and two beta sheets as in the original crambin PDB file., my PDB file doesn't produce ramachandran plot properly I don't know the reason why . Also it doesn't produce new cartoon representation. Can someone help me in fixing this issue ? In both files there is no side chains or hydrogen atoms. first few lines of the second (my file from the code) file has ramachandran angles in radian measure.
1) Crambin.PDB----This is file taken from the internet.
2) crambin0908code.PDB ---This is the file generated by my code.
I am not familiar with C language, however I could help you get the logic. You could look at the following two links that will provide you a detailed guide to generate a code to generate Ramachandran plot.
https://warwick.ac.uk/fac/sci/moac/people/students/peter_cock/python/ramachandran/
http://azevedolab.net/resources/rama_plot_py.pdf
Moreover, there is this python code that might come in handy.
https://github.com/gerdos/PyRAMA/blob/master/rama_lib/ramachandran_calc.py
Dear Vishal, thank you so much... I am able to plot my PDB file in VMD and am able to get the image of the protein ...however vmd doesn't generate ramachandran plot which I am not able to figure it out...
Calculate phi-psi in C itself and plot it. You don't need VMD for doing it right!
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