GARANT Version 2.0
==================

Changes in Version 2.0
----------------------

GARANT has been adapted to work better in conjunction with heteronuclear
3D spectra and routines were implemented to support SAR by NMR. In particular 
the following new commands were introduced (see also corresponding help files):

- define secondary shifts
      defines expected shifts based on 2nd structure.

- filter
      compares peak positions in different spectra in order to identify 
      artifacts or peaks that are folded.

- match
      determines an optimal match between two peak lists.

The following modifications were introduced:

- small differences of the chemical shifts in different spectra are taken 
  into account for scoring resonance assignments.
- the local optimization algorithm was improved. 
- measured peaks whose assignment are fixed with the "fix assignment" command 
  are prevented from being reassigned by the program (in version 1.0 this
  was only the case for the expected peaks).


Installation
------------

To install the program go into the directory garant-2.0 and type the following
commands:
	make clean
	configure
	make
The installation has been tested for Solaris 2 workstations, for IBM RISC
computers and gnu compilers. It needs c, c++ and fortran compilers to be
installed. Adaptions to other types of computers should be made in the configure
script.



File formats
------------

All the files read by GARANT should be in the formats used by XEASY or DIANA.
See also the examples provided in the directort "./examples".


Help system
-----------

After starting garant an online help is available. Typing help will give you a
list of all available help files, typing help <topic> will display the
help file concerning the chosen topic.


Tutorial
--------

There is a short tutorial describing how to use GARANT for automatic resonance
assignments. A Microsoft Word 5.0 version, a rich text format version and a
postscript version is provided in the files tutorial.msword-5.0, tutorial.rtf
and tutorial.ps, respectively. 


Examples
--------

1) To generate the peak list "cbca.peaks" for a CBCA(CO)NHN spectrum for the
protein with sequence "protein.seq" from the known chemical shifts stored in
the file "shifts.prot" type:
	garant genPeaks CBCACONH protein.seq shifts.prot cbca.peaks
see also: helpfile for genPeaks.

2) To generate the peak list "noesy.peaks" for a 2D NOESY spectrum for the
protein with sequence "protein.seq" from the known chemical shifts stored in
the file "shifts.prot" and the structures "protein1.cor", "protein2.cor", ...:
	* make a macro (e.g. called "loadstruc.gar") containing the instructions
		load coordinates protein1.cor
		load coordinates protein2.cor
		...
	* start the garant macro genNoes and follow the instructions
		garant genNoes

3) To generate peak and assignment list for a set of NOESY spectra: make a copy 
of the macro ./maco/asno.gar and modify it according to your needs.

4) To detemine a resonance assignment from homonuclear spectra and, if available,
from the structures or chemical shifts of a homologous protein, make a copy of
the macro ./examples/tend/assigHom.gar and adapt it according to your needs (see
also: tutorial).

5) To determine a resonace assignment from a set of heteronulcear correlated
3D spectra, make a copy of the macros "assignHet.gar" and "writenoesys.gar"
and adapt it accroding to you needs (see also: tutorial).


Acknowledgment
--------------

The transition from GARANT version 1.0 to GARANT version 2.0 was made
possible by support from Hoffmann-La Roche. Many of the improvements in
version 2.0 originated from discussions with Dr. Werner Klaus. 

