My software notes

February 15, 2007

making ramachandran plot by yourself

Filed under: pymol/ molmol,softwares and scripts — kpwu @ 9:34 pm

** NEW on April 19th, 2011****

New post regarding the Ramachandran plot with newer defined ranges is posted at here.

********************************

There are many programs (online or standalone) which can generate ramachandran plots for users when submitting a PDB file. Most people know that beta-strand and alpah-helix have allowed and most favored (most allowed) range, however, the values are not clearly provided by such programs. Here is a list of the 6 high populated regions (95% of the most current PDBs) determined by Ramachandran and his collegues in 70s. Some researchers made better definitions in the last 10 years. I try to obtain their list to make such kind of regions, but failed. Anyway, you can just take the listing 6 regions to make a Ramachadran plot by yourself easily using excel or other graphical program. I am showing an example generated by ProFit (using MacOS X).
ps. The axis labels are wrong, Y is psi, X is phi.

ramachandran-plot-standard.jpg
phi psi
————-
-156.5 91.3
-70.4 91.3
-54.7 112.8
-54.7 173.2
-136.9 173.2
-136.9 155.8
-156.5 135.6
-156.5 91.3
—————–
-180.0 42.9
-140.8 16.1
-86.0 16.1
-74.3 45.6
-74.3 72.5
-44.3 102.0
-44.3 161.1
-46.9 179.9
-180.0 180.0
——————
-180.0 -34.9
-164.3 -42.9
-133.0 -42.9
-109.4 -32.2
-106.9 -21.4
-44.3 -21.4
-44.3 -71.1
-180.0 -71.1
—————-
-156.5 -60.4
-54.7 -60.4
-54.7 -40.2
-100.4 -40.2
-123.9 -51.0
-156.5 -51.0
-156.5 -60.4
—————–
-180.0 -163.8
-75.6 -163.8
-46.9 -180.0
—————–
62.6 14.7
62.6 96.7
45.6 79.2
45.6 26.8
62.6 14.7

reference:
1.from pps:http://www.cryst.bbk.ac.uk/PPS95/course/3_geometry/rama.html
2.I found the definations from xplor. X-PLOR provides an input file to calculate the phi/psi angles and output the values to a mathematica format to generate a Ramachandran plot,here is URL: http://www.ocms.ox.ac.uk/mirrored/xplor/manual/geomanal/ramachandran.math

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4 Comments »

  1. x-axis should be phi
    y-axis should be psi

    Comment by John — October 2, 2008 @ 1:21 am | Reply

  2. Yes, thanks Joe. I did note the wrong labels after I posted this blog.

    Comment by kpwu — October 2, 2008 @ 6:27 am | Reply

  3. Is there a way to plot the Ramachandran plot on Microsoft Excel?

    Comment by Delia — October 17, 2010 @ 2:01 am | Reply

  4. […] time ago, I made a blog article at here to make a record where I can go back to dig information of Ramachandran plot. But the […]

    Pingback by Making Ramachandran plot –II « My software notes — April 19, 2011 @ 7:58 pm | Reply


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