My software notes

May 9, 2011

Examples of Ramachandran plots of residues in helix, strand or coil regions

Filed under: softwares and scripts — kpwu @ 4:56 pm
Tags: , ,

Few weeks ago, I posted a blog that provides a newer collected/organized dataset for the torsional angles of proteins. I played around and try to use GnuPlot 4.4 to make my own Ramachandran plots.

Here are three examples of the residual Ramachandran space regarding to the helical, extend or coil regions. I used STRIDE to define the secondary structural regions and obtain the phi/psi angles.

It is quite convenient to plot my own Ramachandran plots in different purposes using this defined plot. I can now have my customized style. ie. I can have different (background) colors, size of dots and high-resolution output image files.

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4 Comments »

  1. hi
    i know what the plot is and according to your blog i came to know hoe it can be ploted but still one problem is that there is method to plot it
    means there will be some kind of formula so can u tell me what are the formula to calculate these angles please

    Comment by aa — February 21, 2012 @ 1:27 am | Reply

  2. Google helps you to find out the formula: http://en.wikipedia.org/wiki/Dihedral_angle

    Comment by kpwu — February 21, 2012 @ 1:14 pm | Reply

  3. Respected sir,
    Please send me commands to open multiple PDB files one by one automatically,whether it is posible? or i had to type name of each PDB file(1ASE.pdb) present in a folder(PROTEIN) of a drive(‘E:/).

    Comment by vaishu — March 16, 2012 @ 1:08 am | Reply

  4. hi
    did anyone know about EMAIL ID of Mike Harms and Marcin Cieślik(maintaining PDB tools using python.

    Comment by vaishu — March 16, 2012 @ 1:15 am | Reply


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