Index of /ftp/pub/bmrb/timedomain/bmr6011/timedomain_data/t2

[ICO]NameLast modifiedSizeDescription
[DIR]Parent Directory  -  
[ ]text20-Dec-2003 01:26 18  
[ ]test.tab20-Dec-2003 01:26 23K 
[ ]test.points20-Dec-2003 01:26 4.8K 
[ ]test.ass_old20-Dec-2003 01:26 23K 
[ ]test.ass.old20-Dec-2003 01:26 25K 
[ ]test.ass20-Dec-2003 01:26 25K 
[TXT]t2_manual.xmgr20-Dec-2003 01:26 11K 
[ ]t2_manual.ps20-Dec-2003 01:26 24K 
[TXT]t2_garant.xmgr20-Dec-2003 01:26 11K 
[ ]t2_garant.ps20-Dec-2003 01:26 23K 
[TXT]t2.xmgr20-Dec-2003 01:26 13K 
[ ]t2.ps20-Dec-2003 01:26 16K 
[ ]t1p_header20-Dec-2003 01:26 164  
[ ]t1p.values-sort_old20-Dec-2003 01:26 4.7K 
[ ]t1p.values-sort20-Dec-2003 01:26 5.9K 
[ ]t1p.values-final_old20-Dec-2003 01:26 2.7K 
[ ]t1p.values-final220-Dec-2003 01:26 3.1K 
[ ]t1p.values-final20-Dec-2003 01:26 3.0K 
[ ]t1p.values20-Dec-2003 01:26 5.9K 
[ ]t1p.ready_old20-Dec-2003 01:26 7.9K 
[ ]t1p.ready20-Dec-2003 01:26 10K 
[ ]t1p.out20-Dec-2003 01:26 17K 
[ ]t1p.dat20-Dec-2003 01:26 9.0K 
[ ]t1p20-Dec-2003 01:26 6.5K 
[ ]run.sh20-Dec-2003 01:26 82  
[ ]relax.list20-Dec-2003 01:26 49  
[ ]procpar20-Dec-2003 01:26 29K 
[ ]pk.tcl20-Dec-2003 01:26 1.4K 
[ ]pck2clu.awk20-Dec-2003 01:26 97  
[ ]orig.plot20-Dec-2003 01:26 12K 
[ ]nmrDraw.ps20-Dec-2003 01:26 1.4M 
[ ]log20-Dec-2003 01:26 92  
[ ]hsqc.ass20-Dec-2003 01:26 24K 
[ ]ft2_7.com20-Dec-2003 01:26 602  
[ ]ft1.com20-Dec-2003 01:26 497  
[ ]ft.com20-Dec-2003 01:26 878  
[ ]fit.plot20-Dec-2003 01:26 13K 
[ ]fid.com20-Dec-2003 01:26 482  
[ ]fid.Z20-Dec-2003 01:26 5.5M 
[ ]convert.awk20-Dec-2003 01:26 206  
[ ]ass.tcl20-Dec-2003 01:26 2.2K 
[ ]all.com20-Dec-2003 01:26 209  
[ ]T220-Dec-2003 01:26 3.1K 
[ ]22580.all20-Dec-2003 01:26 36K 
[ ]0.PCK20-Dec-2003 01:26 4.4K 
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