(The examples are done on a Intel Mac, Os X system. Red is my input. Blue is the computers responce. Black is a comment)
First, logon one of the iMac computers (as Chemistry 598)
(username and password)
Lets make a directory on our Desktop to put all the NMR data in (from X11, xterm) go get some data to play around with
chm598$ ls
Desktop Library Music Pictures Sites
Documents Movies NMR Public
chm598$ cd Desktop
chm598$ mkdir NMR
chm598$ cd NMR
chm598$ pwd
/Users/chm598/Desktop/NMR
Okay, lets go get some data to play around with.... To minimize vpn and sftp to the secure Sun computer running the 200 MHz Varian NMR Spectrometer, I will transfer NMR data to one of the iMac computers and everyone else can just download it from this one computer.
Specifically, I will load data on iMac MRRC6 (the iMac next to the HP printer). This iMac is unique in that it has a static ip address. The ip is 129.219.53.7 and it has the standard Chemistry 598 account. So, lets all get some NMR data from this computer (I put the data in a folder on the Desktop called CHM598 NMR.
chm598$ sftp chm598@129.219.53.7
sftp> cd Desktop
sftp> cd CHM598_NMR
sftp> mget ./*
sftp> bye
chm598$ ls
1h_test gem300.pdf adc_overflow_1h_test test1.fid
gets all files, but NOT all subdirectories!! this is one reason to zip your NMR data.
Also, you can use Cyberduck (a graphical sftp for Mac) or even better, just afp the drive to your desktop:
Go -> Connect to Server -> afp://129.219.53.7 -> (type u: and p:) -> chm598
Put all Varian NMR data in the folder (directory) on your Desktop called 'NMR'
chm598$ ls
1h_test gem300.pdf water_adc_overflow_test.fid
adc_overflow_1h_test test1.fid water_test.fid
class_test1.fid test_water1.fid
chm598$ pwd
/Users/chm598/Desktop/NMR
chm598$ more 1h_test
-1084 108
-1972 -30
-1840 -322
-1791 -572
-1682 -830
-1536 -1068
-1353 -1286
-1144 -1471
-927 -1614
-685 -1727
-402 -1811
-128 -1849
157 -1846
416 -1803
669 -1723
936 -1594
1148 -1446
1358 -1249
1519 -1041
1654 -803
1751 -550
1814 -265
1832 -14
1816 256
1755 526
1658 776
1505 1038
1342 1239
1134 1430
908 1579
666 1693
406 1771
132 1804
-143 1798
-398 1755
-657 1676
-905 1561
-1136 1407
hit the 'q' key to quit this list
Basically, you can see that this is just an ascii file of numbers (real and imaginary data points of the fid).
Okay, in class we will work on plotting and transforming this data.... For example:
chm598$ cd /Applications/MATLAB73/bin
chm598$ ./matlab -nojvm
< M A T L A B >
Copyright 1984-2006 The MathWorks, Inc.
Version 7.3.0.298 (R2006b)
August 03, 2006
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
>> cd /Users/chm598/Desktop/NMR
>> load 1h_test
>> whos
Name Size Bytes Class Attributes
X1h_test 8192x2 131072 double
ans 1x26 52 char
>> plot(X1h_test(:,1))
Now, plot (:,2)..... next lets start processing this FID step by step in Matlab:
zero=[0:1847].*0;
fid1=[fid1 zero];
lb=5;
fid1a=fid1.*exp(-[1:200]/lb);
spec1=fftshift(fft(conj(fid1a)));
n1=-55
spec1p=phase2(spec1,n1,0);
spec1pr=spec1p(2048:-1:1);
%phase2.m file
%function data = phase2(x,ph0,ph1)
%if nargin < 3
% ph1 = 0;
%end
%if nargin < 2
% ph0 = 0;
%end
%[m n]=size(x);
%i=sqrt(-1);
%z=0:(length(x(1,:))-1);
%z=z/(length(z)-1);
%for r=1:m
%data(r,:)=x(r,:).* exp(i*(ph0/180*pi+ph1/180*pi*z));
%end