I am using the m2p file from https://ringo.ams.stonybrook.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2)
but my ss.jpg is looking pretty sad
I am converting via imagemagick
convert ss.eps ss.jpg
I know I could limit my residue numbers but I'd like to produce something similar to what Dr. Rizzo is able to do.
Hi Brendan! I am using VMD for computing secondary structures. In VMD you can save the output as tml and then using your own code you can convert such files to matrices which can be plotted in a less "sad" way, or as "funny" as you want. You need to use then there Analysis -> Timeline. In Timeline you can calculate desired properties. Just be aware that you get output in frames, not in time (you might need to recompute it). Also the software can take a certain file-size, depending on properties of your computer.
Thank you Inna! I will use VMD then for happy secondary structure graphs!
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