My software notes

March 19, 2012

LigPlot on Mac OS X 10.6

Filed under: mac,softwares and scripts,web — kpwu @ 12:20 am
Tags: ,

A quick note of test of LigPlot on my Mac.

==background ===

If you have ever used the PDBSum service, you may notice many provided useful information including the protein-protein interaction/interface, protein-ligand or protein-DNA (or RNA) interaction/interface, Rama plot, topology and sequence.

For example (see image below), the banner of PDB file (2XUV) entry in PDBSum provides links of “protein, “ligands”, protein-protein interaction” and “clefts” for users to see the detail molecular interactions. When you click the link “ligands” in the banner or the “SO4” link in the “Contents” at left corner, you will see a image generated by LigPlot which shows both hydrophobic and hydrogen bonding interactions between ligand and protein.

=== installation on Mac =====

Following by the instruction described at LigPlot official site, I downloaded the LigPlot binary files (Linux/Unix version) to run it on my iMac (10.6.8).

After uncompressing the hbplus and ligplot file,  as instructed in the “install.doc” text file, 3 steps are essential to make ligplot run well on Mac OS 10.6:

1. user has to manually compile some files in ligplot (GCC must be installed first) :
cc -o ligplot ligplot.c -lm
cc -o hbadd hbadd.c -lm
cc -o dimer dimer.c

2. run “make” in the hbplus to compile all required C files.

3. edit either tcsh, csh or bash shell environment file as suggested in the “install.doc” file.

=== run LigPlot on Mac, an example ===

I have used HADDOCK to generate some protein-RNA docked model and LigPlot was used to see the protein-RNA contacts. Here is the example result:

 

Note: The ligplot author has another specific version called NucPlot to draw the protein-DNA or protein-RNA contacts, I didn’t try it because it just draw the molecular contacts in different style.

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May 16, 2011

statistics of NMR/X-ray determined protein structures in PDB (up to May 10, 2011)

Filed under: web — kpwu @ 4:48 pm
Tags: , , , ,

Two brief plots of protein structures (protein-DNA/RNA/ligand complexes are excluded) determined by either X-ray or NMR. Structures determined by hybrid method are not counted in the two plots. The dataset was obtain from PDB based on its released statistics by May 10th, 2011.

Molecules with sequence length longer than 1200 residues are also excluded. There are 5075 and 2 structures determined by X-ray and NMR methods, respectively in this category.

FYI: I obtained individual numbers from this statistics page at PDB.

Sequence length-dependent distribution plots of X-ray and NMR-determined protein structures.

The magnified NMR section.

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

April 18, 2011

[software] PDB file editor

Filed under: mac,softwares and scripts,web — kpwu @ 9:06 pm
Tags: ,

Bioinformatics.org” hosts a nice GUI-based PDB file editor. The program is written in Java and can run on MS-Win, Linux and Mac OS. Some snapshopts are showing here. I think this is a very friendly program for users who don’t know how to use shell script to change/reset  PDB parameters (e.g. chain ID, beginning number of first residue/atom, remove of heavy atom/water..etc..)

========Program information======

Protein Data Bank (PDB) file editor: web address (http://www.bioinformatics.org/pdbeditor/wiki/Main/HomePage)

=============================

Snapshot 1: target protein coordinate is loaded.

Snapshot 2: the editor window, I reset the beginning residue at 30, and the new ChaiInID is “C”

snapshot 3: the result of new coordinate

April 1, 2011

Agilent’s NMR blog

Filed under: web — kpwu @ 6:05 pm
Tags:

Two weeks, I found Agilent’s NMR blog to introduce their design, concept and technology. This is a quite new website created by  Agilent. Perhaps it is one of the new strategy to interact with most of young NMR users after Agilent acquired Varian in 2009.

The website address is : http://www.spinsights.net/nmr-blog/.

Hope the Agilent scientists can keep sharing innovative and educational information.

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