chemical review on NMR

August 2004

Volume 104, Issue 8

pages 3517-3704

biological NMR

car motto

Find what you love
Love what you find

DinB

The DinB gene and its protein product were first discovered in Walker's lab in 1980, long before scientists knew anything about translesion polymerases. Then graduate student Cynthia Kenyon, now a biologist at University of California, San Francisco who has done groundbreaking work on the genetic basis of aging in worms, systematically identified the genes turned on in bacteria exposed to DNA damaging agents, the so-called SOS response. Kenyon named the damaged-inducible (Din) genes in order of discovery, and DinB was the second one she found.

from
http://www.medicalnewstoday.com/articles/36070.php

SAIC stands for

SAIC stands for Science Applications International Corporation, in case you wonder.

hyperbolic function in awk

Since:

sinh(x)=[exp(x)-exp(-x)]/2
cosh(x)=[exp(x)+exp(-x)]/2
tanh(x)=sinh(x)/cosh(x)

Therefore:

/usr/bin/awk '{print (exp($1)-exp(-$1))/2}' in.dat
/usr/bin/awk '{print (exp($1)+exp(-$1))/2}' in.dat
/usr/bin/awk '{print (exp($1)-exp(-$1))/(exp($1)+exp(-$1))}' in.dat

will give sinh, cosh, and tanh for the data inside in.dat.

An example is below, the first column is input, the rest 3 columns are output of sinh, cosh, and tanh using the above awk commands.
-9.0 -4051.5400 4051.5400 -1.0000
-8.0 -1490.4800 1490.4800 -1.0000
-7.0 -548.3160 548.3170 -1.0000
-6.0 -201.7130 201.7160 -1.0000
-5.0 -74.2032 74.2099 -0.9999
-4.0 -27.2899 27.3082 -0.9993
-3.0 -10.0179 10.0677 -0.9951
-1.0 -1.1752 1.5431 -0.7616
-0.6 -0.6367 1.1855 -0.5371
-0.3 -0.3045 1.0453 -0.2913
0.0 0.0000 1.0000 0.0000
0.3 0.3045 1.0453 0.2913
0.6 0.6367 1.1855 0.5371
1.0 1.1752 1.5431 0.7616
2.0 3.6269 3.7622 0.9640
3.0 10.0179 10.0677 0.9951
4.0 27.2899 27.3082 0.9993
5.0 74.2032 74.2099 0.9999
6.0 201.7130 201.7160 1.0000
7.0 548.3160 548.3170 1.0000
8.0 1490.4800 1490.4800 1.0000
9.0 4051.5400 4051.5400 1.0000

Multiple pages in one postscript file

The following is one postscript file with 3 pages. (I don't know why page 4 doesn't show up).
And the file doesn't always give expected result.
--------------------------
%!PS-Adobe-3.0
%%BoundingBox: 0 0 600 792
%%Page: 1 1
newpath
144 72 moveto
144 232 lineto
stroke
/Times-Roman findfont 30 scalefont setfont
200 200 moveto (page 1)show
showpage
%%Page: 2 2
newpath
144 72 moveto
164 262 lineto
stroke
200 200 moveto (page 2)show
showpage
%%Page: 3 3
newpath
144 72 moveto
184 292 lineto
stroke
200 200 moveto (page 3)show
showpage
%%Page: 4 4
newpath
144 72 moveto
204 322 lineto
stroke
200 200 moveto (page 4)show
showpage
----------------------------------

Looking for a research and/or service position in the field of NMR spectroscopy

I am looking for a research and/or service position in the field of NMR spectroscopy.

Generate publishable quality NMR spectrum by modifying Sparky plot ps file (3)

When postscript looks fine, open it in gimp
in the Load PostScript pop-window, Resolution 100-> 1000,
Width x10, Height x10, eg 826->8260, 1170->11700 then Ok,

It takes time to open, when finish loading, one can Crop image to get rid
of blank region, Scale image to the required size and resolution and save as tif or eps.

One can save a low resolution jpg version by modifying Scale image parameter or select a low Quality number(0-100) in the popup window after trying Save As a new.jpg

Generate publishable quality NMR spectrum by modifying Sparky plot ps file (2)

7, Change peak contour color
"/levelcolor n def" where n could be 0(black), 1(white), 2(gray), 3(red), 4(green) 5(blue), 6(yellow), 7(magenta) 8(cyan) etc.

8, To combine two or more postscript files, simply comment the showpage line and add showpage at the end of the very last postscript file. The relative positions, sizes can be adjusted by modifying some numbers in the combined postscript file.

9, "pt" command from Sparky generate postscript file of the spectra. In order to overlap two or more sets data, ppm/cm should be identical also "rt" make sure all sets with the same ppm range.

10, Useful postscript language like
0.5 0.5 scale (change size)
-200 400 translate (translocation, change position)

0.5 setlinewidth
254 400 moveto 350 400 lineto stroke (draw lines)

11, to write label A, B, ... or any other annotations
gsave
/Helvetica findfont 24 scalefont setfont
-238 685 moveto (A) show
130 685 moveto (B) show
-238 455 moveto (new annotations) show
grestore

Use "gsave ...... grestore" often (make life easier)

Generate publishable quality NMR spectrum by modifying Sparky plot ps file (1)

It is easier to use "vi" in a linux terminal to do the modification.

1, locate setlinewidth, change "1.0 setlinewidth" to "2.0 setlinewidth"
2, If there is label on the figure, change /LabelFont from /Courier to /Helvetica.
3, Label size can be optimized by changing the currentfont value near the end of the file.
4, Label can be moved simply by changing the number associated with the label in the ps file.
5, Axes can be hided by switching true to false near the beginning of the ps file
6, Two postscript files can overlap with different color or be arranged side by side.

music

Music is my hobby. I like listening to music. I like some old popular songs in Chinese, which is my native language. Some songs are just unforgettable. To someone like me, mp3 could be one of the best stuff around nowadays.

(note: mp3 is a music file format. Music from a CD can be converted to mp3 format easily using popular music player. And then you can listen to your favorite music simply by opening the mp3 file on your computer's music player software or any mp3 player, again and again and again ... How nice is that? Can one imagine that 20 years ago?)

Structural biology

For someone who knows structural biology, NMR stands for nuclear magnetic resonance. It is a spectroscopic technique to study the structures and dynamics of molecules at atomic resolution. The molecules can be small organic molecules, or can be macromolecules or biomolecules, such as proteins and nucleic acids. NMR can study samples in both solution state and solid state. I have some expertise on biomolecular solution state NMR. I would like to write down some notes about this topic.

Latex

Recently I started to try using Latex to write things. Already like it very much since I always like plain text format style. I may write down some notes for my own use and hopefully the notes will also benefit other people who are interested in Latex. Of course there are tons of very good articles, manuals, tutorials on the web about Latex. But writing my own notes seems help me learn it faster and it will be handy when I need a Latex command or template or something that I couldn't remember, especially for someone like me who doesn't have a good memory.