Recent Demo Data in the NMRPipe FTP Site
                           July 2, 2006

NOTE WELL: all of the following demos require a version of NMRPipe
retrieved after 7/3/2006.

For the latest NMRPipe FTP instructions and password information, 
send email to delaglio@nih.gov

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MFR Dipolar Coupling and Chemical Shift Homology Search Demo

Review the instructions how to get and install NMRPipe software via FTP.  
When you get the appropriate files from the FTP site according to the 
instructions, get the following three files as well:

   mfr.tar.Z      
   dyn.tar.Z     
   pdbH.tar.Z   

These files should be available when you use the automated installation
script "install.com" -- these additional files will provide tools
for manipulating dipolar couplings and chemical shifts, and also
provide a subset of the PDB structure database with protons added.

More about using the MFR demo can be found in the "mfr/demo/README" file
after installation.

The demo directory also includes several examples of fitting, simulation,
and analysis of dipolar couplings and chemical shifts.

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DYNAMO System for NMR Structure Calculation by Simulated Annealing

Review the instructions how to get and install NMRPipe software via FTP.  
When you get the appropriate files from the FTP site according to the 
instructions, get the following file as well:

   dyn.tar.Z 

If you'd like to have a look at an example of the simulated annealing 
engine DYNAMO, which is under development, see this text in your installation,
which will show you how to run a demo of structure calculation for
ubiquitin:

   dynamo/demos/ubiq/README

Or you can just go to the "dynamo/demos/ubiq" directory, and type
the command "ubiqSA.tcl", and look at the README file later ...

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Automated Nonlinear Lineshape Fitting for 1D, 2D, 3D and Pseudo-3D Data

A script "autoFit.tcl" is now provided with NMRPipe to help automate
the use of the "nlinLS" spectral fitting program.  This autofit script
estimates all required fitting parameters, and also produces a simulated
spectrum and residual.  

An example for fitting 1D data (in this case, actually a projection
from a digitized gel image, not NMR data) can be found in the file
"gel.tar.Z".  Note well that work is also in progress to provide 
a better interactive interface for 1D data. 

An example of fitting 2D data (in this case, IPAP spectra) can be
found in the file "ipap.tar.Z"

An example for automatic fitting of a 2D relaxation series is contained 
in the file "relax.tar.Z" 

An example for automatic fitting of a 2D J-modulated series is contained 
in the file "jmod.tar.Z" 

The automated script seems to work well in many cases.  Note well that 
the success of the analysis depends strongly on the quality of the 
peak table.  Be sure to delete noise peaks, insert unresolved peaks, 
and to inspect and edit the CLUSTID values so that overlapping peaks all 
have the same CLUSTID value. 

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ACME - Measurement of Homonuclear 1H Couplings from Regular 2D COSY Spectra

To use ACME, you will have to get the latest version of NMRPipe from our FTP
site. The tools of ACME are included in the current release. A directory of
sample COSY data and scripts for ACME is provided in the file
"acme.tar.Z" at the FTP site. Once downloaded, the sample data
directory, called "acme", can be extracted with the command:

   zcat acme.tar.Z | tar xvf -

Details on the software can be found in the README file in the
sample directory, or at this site:

   http://spin.niddk.nih.gov/bax/NMRPipe/cosy