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.PCK2021-02-13 18:33 4.4K 
[ ]22580.all2021-02-13 18:32 36K 
[TXT]README.txt2021-02-13 18:33 1.8K 
[ ]T22021-02-13 18:33 3.1K 
[ ]all.com2021-02-13 18:33 209  
[TXT]ass.tcl2021-02-13 18:33 2.2K 
[ ]convert.awk2021-02-13 18:33 206  
[ ]fid.Z2021-02-13 18:32 5.5M 
[ ]fid.com2021-02-13 18:33 482  
[ ]fit.plot2021-02-13 18:32 13K 
[ ]ft.com2021-02-13 18:33 878  
[ ]ft1.com2021-02-13 18:33 497  
[ ]ft2_7.com2021-02-13 18:32 602  
[SND]hsqc.ass2021-02-13 18:33 24K 
[ ]log2021-02-13 18:33 92  
[ ]nmrDraw.ps2021-02-13 18:32 1.4M 
[ ]orig.plot2021-02-13 18:33 12K 
[ ]pck2clu.awk2021-02-13 18:33 97  
[TXT]pk.tcl2021-02-13 18:33 1.4K 
[ ]procpar2021-02-13 18:33 29K 
[ ]relax.list2021-02-13 18:33 49  
[TXT]run.sh2021-02-13 18:33 82  
[ ]t1p2021-02-13 18:33 6.5K 
[ ]t1p.dat2021-02-13 18:33 9.0K 
[ ]t1p.out2021-02-13 18:33 17K 
[ ]t1p.ready2021-02-13 18:33 10K 
[ ]t1p.ready_old2021-02-13 18:33 7.9K 
[ ]t1p.values2021-02-13 18:33 5.9K 
[ ]t1p.values-final2021-02-13 18:33 3.0K 
[ ]t1p.values-final22021-02-13 18:33 3.1K 
[ ]t1p.values-final_old2021-02-13 18:33 2.7K 
[ ]t1p.values-sort2021-02-13 18:33 5.9K 
[ ]t1p.values-sort_old2021-02-13 18:33 4.7K 
[ ]t1p_header2021-02-13 18:33 164  
[ ]t2.ps2021-02-13 18:33 16K 
[ ]t2.xmgr2021-02-13 18:33 13K 
[ ]t2_garant.ps2021-02-13 18:32 23K 
[ ]t2_garant.xmgr2021-02-13 18:33 11K 
[ ]t2_manual.ps2021-02-13 18:33 24K 
[ ]t2_manual.xmgr2021-02-13 18:33 11K 
[SND]test.ass2021-02-13 18:33 25K 
[ ]test.ass.old2021-02-13 18:33 25K 
[ ]test.ass_old2021-02-13 18:33 23K 
[ ]test.points2021-02-13 18:33 4.8K 
[ ]test.tab2021-02-13 18:32 23K 
[ ]text2021-02-13 18:33 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