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

[PARENTDIR]Parent Directory   -  
[   ]0.PCK 2003-12-19 11:26 4.4K 
[   ]22580.all 2003-12-19 11:26 36K 
[   ]T2 2003-12-19 11:26 3.1K 
[   ]all.com 2003-12-19 11:26 209  
[   ]ass.tcl 2003-12-19 11:26 2.2K 
[   ]convert.awk 2003-12-19 11:26 206  
[   ]fid.Z 2003-12-19 11:26 5.5M 
[   ]fid.com 2003-12-19 11:26 482  
[   ]fit.plot 2003-12-19 11:26 13K 
[   ]ft.com 2003-12-19 11:26 878  
[   ]ft1.com 2003-12-19 11:26 497  
[   ]ft2_7.com 2003-12-19 11:26 602  
[   ]hsqc.ass 2003-12-19 11:26 24K 
[   ]log 2003-12-19 11:26 92  
[   ]nmrDraw.ps 2003-12-19 11:26 1.4M 
[   ]orig.plot 2003-12-19 11:26 12K 
[   ]pck2clu.awk 2003-12-19 11:26 97  
[   ]pk.tcl 2003-12-19 11:26 1.4K 
[   ]procpar 2003-12-19 11:26 29K 
[   ]relax.list 2003-12-19 11:26 49  
[   ]run.sh 2003-12-19 11:26 82  
[   ]t1p 2003-12-19 11:26 6.5K 
[   ]t1p.dat 2003-12-19 11:26 9.0K 
[   ]t1p.out 2003-12-19 11:26 17K 
[   ]t1p.ready 2003-12-19 11:26 10K 
[   ]t1p.ready_old 2003-12-19 11:26 7.9K 
[   ]t1p.values 2003-12-19 11:26 5.9K 
[   ]t1p.values-final 2003-12-19 11:26 3.0K 
[   ]t1p.values-final2 2003-12-19 11:26 3.1K 
[   ]t1p.values-final_old 2003-12-19 11:26 2.7K 
[   ]t1p.values-sort 2003-12-19 11:26 5.9K 
[   ]t1p.values-sort_old 2003-12-19 11:26 4.7K 
[   ]t1p_header 2003-12-19 11:26 164  
[   ]t2.ps 2003-12-19 11:26 16K 
[TXT]t2.xmgr 2003-12-19 11:26 13K 
[   ]t2_garant.ps 2003-12-19 11:26 23K 
[TXT]t2_garant.xmgr 2003-12-19 11:26 11K 
[   ]t2_manual.ps 2003-12-19 11:26 24K 
[TXT]t2_manual.xmgr 2003-12-19 11:26 11K 
[   ]test.ass 2003-12-19 11:26 25K 
[   ]test.ass.old 2003-12-19 11:26 25K 
[   ]test.ass_old 2003-12-19 11:26 23K 
[   ]test.points 2003-12-19 11:26 4.8K 
[   ]test.tab 2003-12-19 11:26 23K 
[   ]text 2003-12-19 11:26 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