Processing T1p experiments:
++++++++++++++++++++++++++

In the 1st T1p experiment (with the smallest T1p):
++++++++++++++++++++++++++++++++++++++++++++++++++

 1. nmrDraw (write down the estimated noise and the treshold)
 2. pick peaks
 3. pck2clu.awk:

- getCols test.ass test.points 0 1 2 17 22
- remove the header of test.points

pck2clu.awk test.points > t1p

 4. run.sh: 

- clip header from another t1p and place it in top of this one
- update relax.list

run.sh (produces t1p.out)

 5. getCols

getCols t1p.out t1p.dat 9 10 11 12 13 14 15 0 8

- 9 thru 15: column # with T1p data (always start with 9!!!)
- 0: column # for residue id (always 0!!!)
- 8: column # for absolute intensity for the 1st T1 experiment (always 8!!!)

 6. dataprep:

- remove the header of the t1p.dat

dataprep t1p.dat t1p.ready 7	(7: # of experiments)  

 7. tvalues:

- insert T values (from pulse sequence!) on the top of the t1p.ready (L4 = T/8 has no units!!!):

(Bruker) total relax time (T) values:


70      (vp ph8:r):f2
        (p17*1.5 ph8:r):f2 (p1*1.5 ph4)
        (vp ph8:r):f2
        lo to 70 times 24 
        (p9 ph8:r):f2


T = p9(2m) + 24(1.5p17 + 2vp) (in ms)
T = 2m + 36p17 + 48vp
T : 4.841 14.441 26.441 38.441 60.041 88.841 112.841 139.241 ms

- must have the estimated noise (from nmrDraw)

tvalues t1p.ready t1p.values 7 126 2

(7: # of experiments)
(126: total # of peaks, i.e. including unassigned)
(2: method chosen; always 2!!!)

- at the prompt, write down the estimated noise: 407310

 8. sort -nk 1 t1p.values > t1p.values-sort

 9. update ccc_plot.awk, ccc_norm_plot.awk and plot.sh

10. plot.sh:
(autoscale and file -> write -> parameters -> plot.par)
 
11. convert.awk t1p.values-sort > t1p.values-final

12. rmsd_ave.awk t1p.values-final-modif t1p.values-final-modif


starting XMGR:/usr1/people/cclaudia/apps/xmgr/bin/xmgr&
 
READ-> Block Data-> xydy->12e1->Accept_Close
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -
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[   ]22580.all19-Dec-2003 10:26 36K
[   ]T219-Dec-2003 10:26 3.1K
[   ]all.com19-Dec-2003 10:26 209
[   ]ass.tcl19-Dec-2003 10:26 2.2K
[   ]convert.awk19-Dec-2003 10:26 206
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[   ]fid.com19-Dec-2003 10:26 482
[   ]fit.plot19-Dec-2003 10:26 13K
[   ]ft.com19-Dec-2003 10:26 878
[   ]ft1.com19-Dec-2003 10:26 497
[   ]ft2_7.com19-Dec-2003 10:26 602
[   ]hsqc.ass19-Dec-2003 10:26 24K
[   ]log19-Dec-2003 10:26 92
[   ]nmrDraw.ps19-Dec-2003 10:26 1.4M
[   ]orig.plot19-Dec-2003 10:26 12K
[   ]pck2clu.awk19-Dec-2003 10:26 97
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[   ]procpar19-Dec-2003 10:26 29K
[   ]relax.list19-Dec-2003 10:26 49
[   ]run.sh19-Dec-2003 10:26 82
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[   ]t1p.dat19-Dec-2003 10:26 9.0K
[   ]t1p.out19-Dec-2003 10:26 17K
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[   ]t1p.values19-Dec-2003 10:26 5.9K
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[   ]t1p.values-final_old19-Dec-2003 10:26 2.7K
[   ]t1p.values-sort19-Dec-2003 10:26 5.9K
[   ]t1p.values-sort_old19-Dec-2003 10:26 4.7K
[   ]t1p_header19-Dec-2003 10:26 164
[   ]t2.ps19-Dec-2003 10:26 16K
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[   ]t2_garant.ps19-Dec-2003 10:26 23K
[TXT]t2_garant.xmgr19-Dec-2003 10:26 11K
[   ]t2_manual.ps19-Dec-2003 10:26 24K
[TXT]t2_manual.xmgr19-Dec-2003 10:26 11K
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[   ]test.ass.old19-Dec-2003 10:26 25K
[   ]test.ass_old19-Dec-2003 10:26 23K
[   ]test.points19-Dec-2003 10:26 4.8K
[   ]test.tab19-Dec-2003 10:26 23K
[   ]text19-Dec-2003 10:26 18

Processing T1p experiments:
++++++++++++++++++++++++++

In the 1st T1p experiment (with the smallest T1p):
++++++++++++++++++++++++++++++++++++++++++++++++++

 1. nmrDraw (write down the estimated noise and the treshold)
 2. pick peaks
 3. pck2clu.awk:

- getCols test.ass test.points 0 1 2 17 22
- remove the header of test.points

pck2clu.awk test.points > t1p

 4. run.sh: 

- clip header from another t1p and place it in top of this one
- update relax.list

run.sh (produces t1p.out)

 5. getCols

getCols t1p.out t1p.dat 9 10 11 12 13 14 15 0 8

- 9 thru 15: column # with T1p data (always start with 9!!!)
- 0: column # for residue id (always 0!!!)
- 8: column # for absolute intensity for the 1st T1 experiment (always 8!!!)

 6. dataprep:

- remove the header of the t1p.dat

dataprep t1p.dat t1p.ready 7	(7: # of experiments)  

 7. tvalues:

- insert T values (from pulse sequence!) on the top of the t1p.ready (L4 = T/8 has no units!!!):

(Bruker) total relax time (T) values:


70      (vp ph8:r):f2
        (p17*1.5 ph8:r):f2 (p1*1.5 ph4)
        (vp ph8:r):f2
        lo to 70 times 24 
        (p9 ph8:r):f2


T = p9(2m) + 24(1.5p17 + 2vp) (in ms)
T = 2m + 36p17 + 48vp
T : 4.841 14.441 26.441 38.441 60.041 88.841 112.841 139.241 ms

- must have the estimated noise (from nmrDraw)

tvalues t1p.ready t1p.values 7 126 2

(7: # of experiments)
(126: total # of peaks, i.e. including unassigned)
(2: method chosen; always 2!!!)

- at the prompt, write down the estimated noise: 407310

 8. sort -nk 1 t1p.values > t1p.values-sort

 9. update ccc_plot.awk, ccc_norm_plot.awk and plot.sh

10. plot.sh:
(autoscale and file -> write -> parameters -> plot.par)
 
11. convert.awk t1p.values-sort > t1p.values-final

12. rmsd_ave.awk t1p.values-final-modif t1p.values-final-modif


starting XMGR:/usr1/people/cclaudia/apps/xmgr/bin/xmgr&
 
READ-> Block Data-> xydy->12e1->Accept_Close