My software notes

November 6, 2012

[Modeller] point mutation script

Filed under: softwares and scripts — kpwu @ 10:41 pm
Tags: , ,

Saw a script provided by Modeller that can quickly mutate a point to any other residues.

Here is the linke <Mutate model python script by Modeller>

To use the script, just type command like the following line:
Example: python mutate_model.py 1t29 1699 LEU A > 1t29.log

Where mutate_model.py is the script provided by Modeller
1t29 is the PDB file name
1699 is the position for mutation
LEU is the new residue
A stands for chain number.

I have test this script at Modeller 9v11, it works very well and quickly.

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 But the ranges used in the Ramachandran plot are a bit out of date.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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