Procedure for running GARANT

1. Copy the initial.gar, compare.gar and write.gar default scripts from 
   /data/elgar/cesg/methods/garant/ into /data/elgar/target#/3garant dir, 
   along with [target].seq and [target].prot and peaklists from 2spscan.

2. Make directories 1 (initial.gar output) and 1a,1b,1c (compare.gar output)

3. Execute the first garant run by typing in the main garant dir:
   garant initial 1 [seed] [base_name] >! run1.out &

4. When the first run is complete, begin three comparison runs by typing:
   garant compare 1a 1 [seed] [base_name] >! run1a.out &
                  ^
                  |
     Substitute 1b, 1c and a different seed for other two runs.

5. After verifying the assignments from the first run by looking at strips in 
   hnca, cconh, hncoca, etc. the regions with correct assignments can be fixed 
   using the macro initial_fix.gar. There are three important sets of changes to
   the Garant macro that must be made. (1) Peaklists with verified assignments are 
   named hnca_ass, cconh_ass, etc., and are loaded with the 'load assignments'
   commands near the bottom of the macro. (2) Make sure that a 'reset user assignments' 
   command is executed for each peaklist that contains assignments to be held fixed.
   (3) A section from the initial_fix.gar file below illustrates how to fix assignments 
   for a portion of the sequence, in this case residues 20 through 52. 

# insert here fixed assignments
do i 20 52
   fix assignments "HN($i)"
   fix assignments "N($i)"
#   fix assignments "C($i)"
   fix assignments "CA($i)"
   fix assignments "CB($i)"
end do

# insert here fixed assignments
do i 20 52
   fix assignments "*($i)" 
end do
[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory  -  
[DIR]2/2021-02-13 18:56 -  
[DIR]2b/2021-02-13 18:56 -  
[DIR]3/2021-02-13 18:56 -  
[DIR]1b/2021-02-13 18:56 -  
[DIR]1/2021-02-13 18:56 -  
[ ]write.gar2021-02-13 18:56 1.6K 
[DIR]1a/2021-02-13 18:56 -  
[ ]hncaco.peaks2021-02-13 18:56 19K 
[DIR]2a/2021-02-13 18:56 -  
[ ]hcch.peaks2021-02-13 18:56 87K 
[ ]run3.out2021-02-13 18:56 211K 
[ ]bc019267.prot2021-02-13 18:56 59K 
[ ]hncoca.peaks2021-02-13 18:55 10K 
[ ]comp.gar2021-02-13 18:55 6.8K 
[ ]hnco.peaks2021-02-13 18:55 10K 
[ ]run1a.out2021-02-13 18:55 266K 
[ ]hbhaconh.peaks2021-02-13 18:55 20K 
[ ]run2.out2021-02-13 18:55 249K 
[ ]bc019267.seq2021-02-13 18:55 1.1K 
[ ]hcch_unfold.peaks2021-02-13 18:55 87K 
[ ]hnco_ass.peaks2021-02-13 18:54 9.7K 
[ ]hncacb.peaks2021-02-13 18:54 32K 
[ ]hs15n_new.peaks2021-02-13 18:54 7.7K 
[TXT]README.txt2021-02-13 18:54 1.7K 
[ ]initial_hcch_fix.gar2021-02-13 18:54 5.7K 
[ ]hs15n.peaks2021-02-13 18:54 8.2K 
[ ]hncaco_ass.peaks2021-02-13 18:54 19K 
[ ]hncacb_ass.peaks2021-02-13 18:54 34K 
[ ]initial_hcch.gar2021-02-13 18:54 5.2K 
[ ]initial.gar2021-02-13 18:54 6.7K 
[ ]cconh.peaks2021-02-13 18:54 33K 
[ ]compare_hcch.gar2021-02-13 18:54 6.3K 
[ ]run1.out2021-02-13 18:54 249K 
[ ]write_hcch.gar2021-02-13 18:54 1.5K 
[ ]hnca.peaks2021-02-13 18:53 20K 
[ ]run2b.out2021-02-13 18:53 260K 
[ ]run2a.out2021-02-13 18:53 260K 
Procedure for running GARANT

1. Copy the initial.gar, compare.gar and write.gar default scripts from 
   /data/elgar/cesg/methods/garant/ into /data/elgar/target#/3garant dir, 
   along with [target].seq and [target].prot and peaklists from 2spscan.

2. Make directories 1 (initial.gar output) and 1a,1b,1c (compare.gar output)

3. Execute the first garant run by typing in the main garant dir:
   garant initial 1 [seed] [base_name] >! run1.out &

4. When the first run is complete, begin three comparison runs by typing:
   garant compare 1a 1 [seed] [base_name] >! run1a.out &
                  ^
                  |
     Substitute 1b, 1c and a different seed for other two runs.

5. After verifying the assignments from the first run by looking at strips in 
   hnca, cconh, hncoca, etc. the regions with correct assignments can be fixed 
   using the macro initial_fix.gar. There are three important sets of changes to
   the Garant macro that must be made. (1) Peaklists with verified assignments are 
   named hnca_ass, cconh_ass, etc., and are loaded with the 'load assignments'
   commands near the bottom of the macro. (2) Make sure that a 'reset user assignments' 
   command is executed for each peaklist that contains assignments to be held fixed.
   (3) A section from the initial_fix.gar file below illustrates how to fix assignments 
   for a portion of the sequence, in this case residues 20 through 52. 

# insert here fixed assignments
do i 20 52
   fix assignments "HN($i)"
   fix assignments "N($i)"
#   fix assignments "C($i)"
   fix assignments "CA($i)"
   fix assignments "CB($i)"
end do

# insert here fixed assignments
do i 20 52
   fix assignments "*($i)" 
end do