My software notes

April 19, 2011

Making Ramachandran plot –II

Long 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 But the ranges used in the Ramachandran plot are a bit out of date. The Richardson group has a publication in 2003 (Structure validation by Calpha geometry: phi,psi and Cbeta deviation at Proteins) showing a new defined favored and allowed psi/phi ranges.

I learned the defined ranges from a java script provided by an online article by Peter N. Robinson and use the defined values to make an GnuPlot (good for 4.o or above) script to generate my own Ramachandran plot. Robinson’s Java script is easy to make a Ramanchandran plot,too.

Another useful program/tool-kit is the pdb-tools which is currently maintained by Mike Harms and Marcin Cieślik. The pdb-tools provides more than 30 python scripts to dissect, analyze and re-generate the PDB file. I use one of the script “pdb_torsion.py” to generate the psi/phi angles of my calculated proteins.

Now, I have enough tools to get the torsion angles and generate tons of images of Ramachandran plots of calculated proteins automatically. Hooray~.

The result is shown here on the left side. Another figure is generated by MOLMOL in order to provide comparable defined ranges and calculated psi/phi angles.

The ranges I got for Peter N. Robinson’s Java script are posted at here,too.

===  favored (red) regions ====
region 1:

        -177.5 -180.0
        -177.5 -177.5
        -172.5 -177.5
        -172.5 -172.5
        -167.5 -172.5
        -167.5 -167.5
        -127.5 -167.5
        -127.5 -172.5
        -97.5 -172.5
        -97.5 -167.5
        -77.5 -167.5
        -77.5 -172.5
        -72.5 -172.5
        -72.5 -177.5
        -67.5 -177.5
        -67.5 -180.0
region 2:
        57.5 67.5
        57.5 62.5
        62.5 62.5
        62.5 57.5
        67.5 57.5
        67.5 47.5
        72.5 47.5
        77.5 32.5
        77.5 2.5
        62.5 2.5
        62.5 7.5
        57.5 7.5
        57.5 12.5
        52.5 12.5
        52.5 22.5
        47.5 22.5
        47.5 27.5
        42.5 27.5
        42.5 37.5
        37.5 37.5
        37.5 62.5
        42.5 62.5
        42.5 67.5
        57.5 67.5
region 3:
        -62.5 180.0
        -62.5 172.5
        -57.5 172.5
        -57.5 167.5
        -52.5 167.5
        -52.5 157.5
        -47.5 157.5
        -47.5 147.5
        -42.5 147.5
        -42.5 137.5
        -37.5 137.5
        -37.5 122.5
        -42.5 122.5
        -42.5 117.5
        -47.5 117.5
        -47.5 112.5
        -57.5 112.5
        -57.5 107.5
        -62.5 107.5
        -62.5 102.5
        -67.5 102.5
        -67.5 97.5
        -72.5 97.5
        -72.5 62.5
        -77.5 62.5
        -77.5 52.5
        -87.5 52.5
        -87.5 47.5
        -92.5 47.5
        -92.5 52.5
        -97.5 52.5
        -97.5 67.5
        -102.5 67.5
        -102.5 77.5
        -107.5 77.5
        -107.5 82.5
        -112.5 82.5
        -112.5 72.5
        -117.5 72.5
        -117.5 62.5
        -122.5 62.5
        -122.5 52.5
        -127.5 52.5
        -127.5 47.5
        -112.5 47.5
        -112.5 42.5
        -102.5 42.5
        -102.5 37.5
        -92.5 37.5
        -92.5 32.5
        -87.5 32.5
        -87.5 22.5
        -82.5 22.5
        -82.5 17.5
        -77.5 17.5
        -77.5 12.5
        -67.5 12.5
        -67.5 7.5
        -62.5 7.5
        -62.5 2.5
        -57.5 2.5
        -57.5 -7.5
        -52.5 -7.5
        -52.5 -12.5
        -47.5 -12.5
        -47.5 -22.5
        -42.5 -22.5
        -42.5 -32.5
        -37.5 -32.5
        -37.5 -62.5
        -42.5 -62.5
        -42.5 -67.5
        -77.5 -67.5
        -77.5 -62.5
        -117.5 -62.5
        -117.5 -57.5
        -122.5 -57.5
        -122.5 -47.5
        -127.5 -47.5
        -127.5 -37.5
        -132.5 -37.5
        -132.5 -17.5
        -137.5 -17.5
        -137.5 2.5
        -142.5 2.5
        -142.5 32.5
        -137.5 32.5
        -137.5 52.5
        -142.5 52.5
        -142.5 57.5
        -147.5 57.5
        -147.5 67.5
        -152.5 67.5
        -152.5 77.5
        -147.5 77.5
        -147.5 87.5
        -152.5 87.5
        -152.5 97.5
        -157.5 97.5
        -157.5 112.5
        -162.5 112.5
        -162.5 122.5
        -167.5 122.5
        -167.5 132.5
        -172.5 132.5
        -172.5 142.5
        -180.0 142.5
===== allowed (blue) region====
region 1
        -180.0 -147.5
        -177.5 -147.5
        -167.5 -147.5
        -167.5 -142.5
        -157.5 -142.5
        -157.5 -137.5
        -147.5 -137.5
        -147.5 -132.5
        -142.5 -132.5
        -142.5 -127.5
        -147.5 -127.5
        -147.5 -97.5
        -152.5 -97.5
        -152.5 -92.5
        -157.5 -92.5
        -157.5 -82.5
        -162.5 -82.5
        -162.5 -52.5
        -157.5 -52.5
        -157.5 -37.5
        -162.5 -37.5
        -162.5 -7.5
        -167.5 -7.5
        -167.5 32.5
        -172.5 32.5
        -172.5 52.5
        -177.5 52.5
        -177.5 77.5
        -180.0 77.5
region 2:
        -42.5 180.0
        -42.5 172.5
        -42.5 172.5
        -37.5 172.5
        -37.5 167.5
        -32.5 167.5
        -32.5 157.5
        -27.5 157.5
        -27.5 147.5
        -22.5 147.5
        -22.5 127.5
        -17.5 127.5
        -17.5 112.5
        -22.5 112.5
        -22.5 107.5
        -27.5 107.5
        -27.5 102.5
        -32.5 102.5
        -32.5 97.5
        -47.5 97.5
        -47.5 92.5
        -52.5 92.5
        -52.5 72.5
        -57.5 72.5
        -57.5 42.5
        -62.5 42.5
        -62.5 27.5
        -57.5 27.5
        -57.5 22.5
        -52.5 22.5
        -52.5 12.5
        -47.5 12.5
        -47.5 7.5
        -42.5 7.5
        -42.5 2.5
        -37.5 2.5
        -37.5 -7.5
        -32.5 -7.5
        -32.5 -12.5
        -27.5 -12.5
        -27.5 -27.5
        -22.5 -27.5
        -22.5 -47.5
        -17.5 -47.5
        -17.5 -67.5
        -22.5 -67.5
        -22.5 -77.5
        -27.5 -77.5
        -27.5 -82.5
        -47.5 -82.5
        -47.5 -87.5
        -77.5 -87.5
        -77.5 -92.5
        -87.5 -92.5
        -87.5 -112.5
        -92.5 -112.5
        -92.5 -122.5
        -97.5 -122.5
        -97.5 -137.5
        -92.5 -137.5
        -92.5 -142.5
        -82.5 -142.5
        -82.5 -147.5
        -72.5 -147.5
        -72.5 -152.5
        -67.5 -152.5
        -67.5 -157.5
        -62.5 -157.5
        -62.5 -162.5
        -57.5 -162.5
        -57.5 -167.5
        -52.5 -167.5
        -52.5 -172.5
        -47.5 -172.5
        -47.5 -177.5
        -42.5 -177.5
        -42.5 -180.0
 region 3:
        82.5 57.5
        87.5 57.5
        87.5 42.5
        92.5 42.5
        92.5 22.5
        97.5 22.5
        97.5 -17.5
        92.5 -17.5
        92.5 -22.5
        87.5 -22.5
        87.5 -27.5
        82.5 -27.5
        82.5 -37.5
        87.5 -37.5
        87.5 -47.5
        92.5 -47.5
        92.5 -57.5
        87.5 -57.5
        87.5 -67.5
        82.5 -67.5
        82.5 -72.5
        77.5 -72.5
        77.5 -77.5
        62.5 -77.5
        62.5 -72.5
        57.5 -72.5
        57.5 -67.5
        52.5 -67.5
        52.5 -37.5
        57.5 -37.5
        57.5 -27.5
        62.5 -27.5
        62.5 -22.5
        57.5 -22.5
        57.5 -12.5
        52.5 -12.5
        52.5 -7.5
        47.5 -7.5
        47.5 -2.5
        42.5 -2.5
        42.5 2.5
        37.5 2.5
        37.5 12.5
        32.5 12.5
        32.5 22.5
        27.5 22.5
        27.5 32.5
        22.5 32.5
        22.5 47.5
        17.5 47.5
        17.5 67.5
        22.5 67.5
        22.5 77.5
        27.5 77.5
        27.5 82.5
        32.5 82.5
        32.5 87.5
        47.5 87.5
        47.5 92.5
        67.5 92.5
        67.5 87.5
        72.5 87.5
        72.5 82.5
        77.5 82.5
        77.5 77.5
        82.5 77.5
        82.5 57.5
 region 4:
        72.5 -102.5
        72.5 -112.5
        77.5 -112.5
        77.5 -157.5
        72.5 -157.5
        72.5 -180.0
        57.5 -180.0
        57.5 -167.5
        52.5 -167.5
        52.5 -162.5
        47.5 -162.5
        47.5 -157.5
        42.5 -157.5
        42.5 -152.5
        37.5 -152.5
        37.5 -142.5
        32.5 -142.5
        32.5 -107.5
        37.5 -107.5
        37.5 -102.5
        42.5 -102.5
        42.5 -97.5
        52.5 -97.5
        52.5 -92.5
        62.5 -92.5
        62.5 -97.5
        67.5 -97.5
        67.5 -102.5
        72.5 -102.5
 region 5:
        77.5 180.0
        77.5 162.5
        82.5 162.5
        82.5 147.5
        72.5 147.5
        72.5 157.5
        67.5 157.5
        67.5 167.5
        62.5 167.5
        62.5 180.0
 region 6:
        162.5 180.0
        162.5 147.5
        167.5 147.5
        167.5 132.5
        172.5 132.5
        172.5 117.5
        177.5 117.5
        177.5 77.5
        180.0 77.5
 region 7:
        162.5 -180.0
        162.5 -177.5
        167.5 -177.5
        167.5 -167.5
        172.5 -167.5
        172.5 -157.5
        177.5 -157.5
        177.5 -147.5
        180.0 -147.5

=========== end of defined values in ramachandran plot ==========

The Gnuplot script is posted at here, in case of missing file in my disc.
The torsion angle file is used as “phipsi.txt” in this script.

==== plot.gnu, use /path/gnuplot plot.gnu to run =======
set terminal png
set output “rama.png”
set noautoscale
set xrange [-180:180]
set xtics -180,30,180 out nomirror
set yrange [-180:180]
set ytics -180,30,180 out nomirror
set tic scale 0.8
set xlabel “phi”
set ylabel “psi”
set arrow from 0, -180 to 0, 180 nohead lw 0.3
set arrow from -180, 0 to 180,0 nohead lw 0.3
set pointsize 0.6
unset key
# LINE COLORS, STYLES
# type ‘test’ to see the colors and point types available.
# Differs from x11 to postscript
# lt chooses a particular line type: -1=black 1=red 2=grn 3=blue 4=purple 5=aqua 6=brn 7=orange 8=light-brn
# lt must be specified before pt for colored points
#
plot “region1” with l lt 1, “region2” with l lt 1, “region3” with l lt 1, “region-w1” with l lt 3, “region-w2” with l lt 3,
“region-w3” with l lt 3, “region-w4” with l lt 3, “region-w5″ with l lt 3,”region-w6” with l lt 3, “region-w7” with l lt 3,
“phipsi.txt” lt -1 pt 5

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7 Comments »

  1. […] ** NEW post regarding the Ramachandran plot is at here“ […]

    Pingback by making ramachandran plot by yourself « My software notes — April 19, 2011 @ 10:31 pm | Reply

  2. […] weeks ago, I posted a blog that provides a newer collected/organized dataset for the torsional angles of proteins. I played […]

    Pingback by Examples of Ramachandran plots of residues in helix, strand or coil regions « My software notes — May 9, 2011 @ 4:56 pm | Reply

  3. This information was really very helpful for understanding how to define range for making our own ramachandran plot. Thanks for the useful post.
    I have one question. Don’t you think that the blue and red regions (especially the biggest blue and biggest red region) defined by the phi psi values are covering more area on ramachandran map as compared to the ramachandran map generated by molmol which seems more realistic map which is on right side). If this is so then using the above phi psi value and ranges will be approximate and that too less valuable as compared to more realistic ranges.
    Do you know any other source or reference where the more specific ranges are defined?
    Your advice will be really help me in my work.

    Thanks in advance 🙂

    Comment by sandeep singh — April 19, 2012 @ 6:54 am | Reply

    • The blue/red regions are defined by Richardson’s paper (See the link in my post) and I think that’s the most up-to-date statistical analysis of Ramachandran plot based on a lot high quality/resolution proteins. If I am right, MOLMOL uses the ranges same as Procheck does. That old ranges were defined based on few hundreds structures more than 10 (15?) years ago. I would say the ranges defined by MolProbity are more reliable (to me).

      In my experiences, most of phi/psi values should located in the “red” (most favored) regions which is commonly seen in crystal structures (97-99% of residues).

      –any other source or reference regarding the regions? Sorry I don’t know exactly examples. If I am doing this project, I might check Ad Bax’s TALOS/TALOS+/SPARTA and David Wishart’s PREDICTOR to know if they have some “special”/self-defined ranges.

      Good lucks.

      Comment by kpwu — April 19, 2012 @ 11:34 pm | Reply

  4. Thanks for the answer. Kindly provide me one more information, as i am a starter in this field of protein structure and you are having more experience which can help me.
    Is there any script or program which takes input as phi and psi value and gives information that the phi psi you entered is within red/blue region or is an outlier
    I know the above ranges given can help to create script for it, but it will require time and programming skills. But if already someone has made it then its better to use it and credit him/her.
    Also I have searched in internet. There are programs which take pdb file as input and give make ramachandran map but my requirement is that input should be phi and psi value and output should be information whether that phi-psi point is an outlier in rama map or is within red/blue region.
    Also if there is no such script available do you have any reference where i can know how to modify some available scripts for my purpose.

    Comment by sandeep singh — April 20, 2012 @ 3:34 am | Reply

  5. can u tell me how to plot ramachandran by using java ..can u give me the source code it is vry useful for my project……

    Comment by Sathya Muthusamy — June 8, 2012 @ 12:59 am | Reply

  6. I don’t know Java, there are a bunch of free source code available online, some are introduced in my blog articles. I believe it’s not hard if you could try them first.

    Comment by kpwu — June 8, 2012 @ 1:03 am | Reply


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