Hello, I used PyTraj to plot a Ramachandran plot for a protein, but the plot contains so many residues that it’s difficult to analyze. Is there a more straightforward way to interpret the plot and predict the protein’s secondary structure? I also tried using VMD, which generates residue-specific plots, but as a beginner, I find it quite confusing. Any advice please?
VMD generates secondary structures for proteins and peptides in time. Structures are visualized directly. You can also select an option of writing all results in a file which you can later analyze with own codes. It is important to read about algorithms which are used for analyzing secondary structures in order to have no confusion. It is impossible to give any other exact answers to your questions as you do not specify what is confusing you exactly. You shall show plots and point out what is confusing.
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