Index of /ftp/pub/bmrb/entry_directories/bmr19213/timedomain_data/ass

[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory   -  
[ ]000-readme 2021-02-13 20:15 662  
[TXT]2O9C.pdb 2021-02-13 20:14 298K 
[ ]2nd_inCS.tab 2021-02-13 20:13 41K 
[ ]13C_NMR_heme.pdf 2021-02-13 20:14 1.0M 
[TXT]blast.txt 2021-02-13 20:15 1.7K 
[ ]bmrb2talos 2021-02-13 20:14 3.3K 
[ ]bmrb2talos.awk 2021-02-13 20:14 1.6K 
[ ]cbca 2021-02-13 20:14 132K 
[ ]cco 2021-02-13 20:15 153K 
[DIR]ccpn/ 2021-02-13 20:13 -  
[TXT]clustal.txt 2021-02-13 20:15 1.9K 
[ ]diff_pr_pfr.tcl 2021-02-13 20:15 5.5K 
[ ]diff_pr_pfr_hn.tcl 2021-02-13 20:15 4.5K 
[ ]getseq.tcl 2021-02-13 20:14 1.7K 
[ ]hbha 2021-02-13 20:14 127K 
[ ]hcco 2021-02-13 20:14 186K 
[ ]hncacb 2021-02-13 20:15 187K 
[ ]hnco 2021-02-13 20:15 70K 
[ ]hnco.sort 2021-02-13 20:14 58K 
[ ]hnco_no_conf 2021-02-13 20:14 58K 
[ ]hnco_wrong 2021-02-13 20:14 70K 
[ ]merge_pipp.tcl 2021-02-13 20:14 8.3K 
[ ]methines 2021-02-13 20:14 88  
[TXT]model.pdb 2021-02-13 20:15 80K 
[ ]model.pse 2021-02-13 20:16 307K 
[TXT]model_h.pdb 2021-02-13 20:15 182K 
[TXT]model_project.pdb 2021-02-13 20:15 176K 
[ ]pipe2pipp.tcl 2021-02-13 20:15 5.9K 
[ ]pipe2pipp_sc.tcl 2021-02-13 20:15 8.0K 
[ ]pipp2col.tcl 2021-02-13 20:15 3.3K 
[ ]pipp2prot.tcl 2021-02-13 20:15 4.7K 
[ ]pipp2talos.tcl 2021-02-13 20:16 3.3K 
[ ]pixj-01-ccc.shifts 2021-02-13 20:15 46K 
[TXT]pixj-01-ccc.shifts-d..>2021-02-13 20:13 7.4K 
[ ]pixj-01-ccc.shifts_c..>2021-02-13 20:14 46K 
[ ]pixj-01-ccc.shifts_c..>2021-02-13 20:14 40K 
[ ]pixj-01-ccc.shifts_c..>2021-02-13 20:15 41K 
[ ]pixj-01-ccc.shifts_c..>2021-02-13 20:14 41K 
[ ]pixj-01-ccc.shifts_c..>2021-02-13 20:14 41K 
[ ]pixj-02.shifts 2021-02-13 20:14 46K 
[ ]pixj-02.shifts_col 2021-02-13 20:14 42K 
[ ]pixj-02.shifts_sort 2021-02-13 20:14 42K 
[ ]pixj-03.shifts 2021-02-13 20:15 49K 
[ ]pixj-03.shifts_col 2021-02-13 20:15 44K 
[ ]pixj-03.shifts_sort 2021-02-13 20:15 33K 
[ ]pixj-04.shifts 2021-02-13 20:15 52K 
[ ]pixj-04.shifts-p4 2021-02-13 20:15 51K 
[ ]pixj-04.shifts_col 2021-02-13 20:14 44K 
[ ]pixj-04.shifts_sort 2021-02-13 20:14 44K 
[ ]pixj-05.shifts 2021-02-13 20:15 52K 
[ ]pixj-05.shifts_col 2021-02-13 20:14 44K 
[ ]pixj-05.shifts_sorted 2021-02-13 20:14 33K 
[ ]pixj-06.shifts 2021-02-13 20:15 52K 
[ ]pixj-06.shifts_col 2021-02-13 20:13 45K 
[ ]pixj-06.shifts_sort 2021-02-13 20:15 45K 
[ ]pixj-06.shifts_sorted 2021-02-13 20:14 34K 
[ ]pixj-07-arg.prot 2021-02-13 20:14 46K 
[ ]pixj-07-arg.shifts 2021-02-13 20:14 52K 
[ ]pixj-07-arg.shifts-bak 2021-02-13 20:15 52K 
[ ]pixj-07-arg.shifts_col 2021-02-13 20:14 45K 
[ ]pixj-07-arg.shifts_sort2021-02-13 20:15 45K 
[ ]pixj-07-arg.shifts_s..>2021-02-13 20:15 34K 
[ ]pixj.prot 2021-02-13 20:15 41K 
[ ]pixj.shifts 2021-02-13 20:13 41K 
[ ]pixj.tab 2021-02-13 20:15 24K 
[ ]pixj.tab_old 2021-02-13 20:14 24K 
[ ]pixj_bb.pipp 2021-02-13 20:15 28K 
[ ]pixj_blast_align_syb..>2021-02-13 20:14 2.9K 
[ ]pixj_pg.tab 2021-02-13 20:15 25K 
[ ]pixj_pvb_shifts 2021-02-13 20:13 2.1K 
[ ]pixj_pvb_shifts.sort 2021-02-13 20:14 2.1K 
[ ]pvb_ass.col 2021-02-13 20:15 868  
[ ]seq 2021-02-13 20:14 1.1K 
[ ]seq.pine 2021-02-13 20:15 341  
[ ]seq.talos 2021-02-13 20:14 244  
[TXT]seq.txt 2021-02-13 20:15 1.0K 
[ ]seq.xplor 2021-02-13 20:15 684  
[TXT]seq_bmrb.txt 2021-02-13 20:15 180  
[TXT]seq_one_line.txt 2021-02-13 20:15 171  
[TXT]seq_pine_1letter.txt 2021-02-13 20:14 341  
[DIR]strip_pb/ 2021-02-13 20:15 -  
[DIR]strip_pb_all/ 2021-02-13 20:15 -  
PixJ:

Me-PCB labeled CH vs. CH/CH2/CH3 - no difference...

- strong signal in 5-ALA 13C @ 63/3.7 also present in the Me-PCB, therefore it's C12

- signal at 6.1/102.2 in Pb dissapears in Pg

***

sort +30 hnco > hnco.sort

delete entries like xY35 (conf. exch.)

sort +0n hnco.sort > junk

bb only (not needed):
pipe2pipp.tcl > pixj_bb.pipp 

*** combine all:

1. use a maxDiff(HN) of 0.02 ppm to check for errors
2. change it to 0.1 ppm to use the hnco amide shifts):

pipe2pipp_sc.tcl > pixj.shifts

*** talos+:

pipp2talos.tcl pixj.shifts > pixj.tab

talos+ -in pixj.tab -check
Chemical shift outlier checking...
   14 A   C Secondary Shift:    3.993    Limit:    3.727
   17 E   C Secondary Shift:   -5.660    Limit:   -4.435
   18 T  CA Secondary Shift:    4.859    Limit:    4.660
   20 V   N Secondary Shift:  -13.121    Limit:  -11.301
   29 C  HA Secondary Shift:    1.132    Limit:    1.047
   29 C  CA Secondary Shift:   -4.142    Limit:   -3.445
   31 R  HA Secondary Shift:    1.171    Limit:    1.047
   32 V  HA Secondary Shift:    1.062    Limit:    1.047
   33 I  HA Secondary Shift:    1.099    Limit:    1.047
   41 Y  HA Secondary Shift:   -1.301    Limit:   -1.080
   41 Y  CB Secondary Shift:   -4.108    Limit:   -3.765
   43 G   C Secondary Shift:   -3.941    Limit:   -3.725
   48 E  CB Secondary Shift:    6.588    Limit:    6.317
   50 V  HA Secondary Shift:    1.241    Limit:    1.047
   50 V  CA Secondary Shift:   -3.643    Limit:   -3.445
   54 W  CA Secondary Shift:   -3.686    Limit:   -3.445
   64 D  CA Secondary Shift:   -3.840    Limit:   -3.445
   67 F  CA Secondary Shift:    5.265    Limit:    4.660
   72 V  CA Secondary Shift:    5.743    Limit:    4.660
   74 A   C Secondary Shift:    4.712    Limit:    3.727
   75 Y  CA Secondary Shift:    6.048    Limit:    4.660
   79 R   C Secondary Shift:   -5.300    Limit:   -4.435
  100 R  CA Secondary Shift:    5.178    Limit:    4.660
  104 V  HA Secondary Shift:   -1.120    Limit:   -1.080
  107 N  HA Secondary Shift:    1.260    Limit:    1.047
  107 N   C Secondary Shift:   -4.669    Limit:   -4.435
  110 V  HA Secondary Shift:    1.240    Limit:    1.047
  110 V  CA Secondary Shift:   -5.517    Limit:   -3.445
  111 P  CB Secondary Shift:    2.783    Limit:    2.771
  119 F   N Secondary Shift:   10.711    Limit:   10.047
  120 G   C Secondary Shift:   -5.724    Limit:   -3.725
  123 I  HA Secondary Shift:    1.162    Limit:    1.047
  125 H  HA Secondary Shift:    1.323    Limit:    1.047
  125 H  CA Secondary Shift:   -3.473    Limit:   -3.445
  125 H  CB Secondary Shift:    6.629    Limit:    6.317
  127 A   N Secondary Shift:   10.407    Limit:   10.047
  131 R   C Secondary Shift:   -4.961    Limit:   -4.435
  135 E  CA Secondary Shift:    4.861    Limit:    4.660
  138 I  CA Secondary Shift:    5.163    Limit:    4.660
  147 T  CA Secondary Shift:    4.735    Limit:    4.660
  149 S  CA Secondary Shift:    5.406    Limit:    4.660
  154 R   C Secondary Shift:   -5.478    Limit:   -4.435

Chemical shift referencing checking...
  Estimated CA shift referencing offset   0.163 ppm (fitting error:  0.121, size:  75)
  Estimated CB shift referencing offset   0.163 ppm (fitting error:  0.121, size:  75)
  Estimated HA shift referencing offset  -0.017 ppm (fitting error:  0.044, size:  67)
  Estimated C' shift referencing offset  -0.781 ppm (fitting error:  0.201, size:  64)

pipp2col.tcl pixj-01-ccc.shifts_corrected > pixj-01-ccc.shifts_corrected.col