Index of /ftp/pub/bmrb/timedomain/bmr19214/timedomain_data/ass

[ICO]NameLast modifiedSizeDescription
[DIR]Parent Directory  -  
[ ]000-readme28-Jun-2014 01:27 662  
[TXT]2O9C.pdb28-Jun-2014 01:27 298K 
[ ]2nd_inCS.tab28-Jun-2014 01:27 41K 
[ ]13C_NMR_heme.pdf28-Jun-2014 01:27 1.0M 
[TXT]blast.txt28-Jun-2014 01:27 1.7K 
[ ]bmrb2talos28-Jun-2014 01:27 3.3K 
[ ]bmrb2talos.awk28-Jun-2014 01:27 1.6K 
[ ]cbca28-Jun-2014 01:27 132K 
[ ]cco28-Jun-2014 01:27 153K 
[DIR]ccpn/28-Jun-2014 01:27 -  
[TXT]clustal.txt28-Jun-2014 01:27 1.9K 
[ ]diff_pr_pfr.tcl28-Jun-2014 01:28 5.5K 
[ ]diff_pr_pfr_hn.tcl28-Jun-2014 01:27 4.5K 
[ ]getseq.tcl28-Jun-2014 01:27 1.7K 
[ ]hbha28-Jun-2014 01:27 127K 
[ ]hcco28-Jun-2014 01:27 186K 
[ ]hncacb28-Jun-2014 01:27 187K 
[ ]hnco28-Jun-2014 01:27 70K 
[ ]hnco.sort28-Jun-2014 01:27 58K 
[ ]hnco_no_conf28-Jun-2014 01:27 58K 
[ ]hnco_wrong28-Jun-2014 01:27 70K 
[ ]merge_pipp.tcl28-Jun-2014 01:27 8.3K 
[ ]methines28-Jun-2014 01:27 88  
[TXT]model.pdb28-Jun-2014 01:27 80K 
[ ]model.pse28-Jun-2014 01:27 307K 
[TXT]model_h.pdb28-Jun-2014 01:28 182K 
[TXT]model_project.pdb28-Jun-2014 01:27 176K 
[ ]pipe2pipp.tcl28-Jun-2014 01:27 5.9K 
[ ]pipe2pipp_sc.tcl28-Jun-2014 01:27 8.0K 
[ ]pipp2col.tcl28-Jun-2014 01:27 3.3K 
[ ]pipp2prot.tcl28-Jun-2014 01:27 4.7K 
[ ]pipp2talos.tcl28-Jun-2014 01:27 3.3K 
[ ]pixj-01-ccc.shifts28-Jun-2014 01:27 46K 
[TXT]pixj-01-ccc.shifts-differences28-Jun-2014 01:27 7.4K 
[ ]pixj-01-ccc.shifts_corrected28-Jun-2014 01:27 46K 
[ ]pixj-01-ccc.shifts_corrected.col28-Jun-2014 01:27 40K 
[ ]pixj-01-ccc.shifts_corrected.sort28-Jun-2014 01:28 41K 
[ ]pixj-01-ccc.shifts_corrected.sort228-Jun-2014 01:27 41K 
[ ]pixj-01-ccc.shifts_corrected.sortwrong28-Jun-2014 01:27 41K 
[ ]pixj-02.shifts28-Jun-2014 01:28 46K 
[ ]pixj-02.shifts_col28-Jun-2014 01:27 42K 
[ ]pixj-02.shifts_sort28-Jun-2014 01:27 42K 
[ ]pixj-03.shifts28-Jun-2014 01:27 49K 
[ ]pixj-03.shifts_col28-Jun-2014 01:27 44K 
[ ]pixj-03.shifts_sort28-Jun-2014 01:27 33K 
[ ]pixj-04.shifts28-Jun-2014 01:27 52K 
[ ]pixj-04.shifts-p428-Jun-2014 01:27 51K 
[ ]pixj-04.shifts_col28-Jun-2014 01:28 44K 
[ ]pixj-04.shifts_sort28-Jun-2014 01:27 44K 
[ ]pixj-05.shifts28-Jun-2014 01:27 52K 
[ ]pixj-05.shifts_col28-Jun-2014 01:27 44K 
[ ]pixj-05.shifts_sorted28-Jun-2014 01:27 33K 
[ ]pixj-06.shifts28-Jun-2014 01:27 52K 
[ ]pixj-06.shifts_col28-Jun-2014 01:27 45K 
[ ]pixj-06.shifts_sort28-Jun-2014 01:27 45K 
[ ]pixj-06.shifts_sorted28-Jun-2014 01:27 34K 
[ ]pixj-07-arg.prot28-Jun-2014 01:27 46K 
[ ]pixj-07-arg.shifts28-Jun-2014 01:27 52K 
[ ]pixj-07-arg.shifts-bak28-Jun-2014 01:27 52K 
[ ]pixj-07-arg.shifts_col28-Jun-2014 01:27 45K 
[ ]pixj-07-arg.shifts_sort28-Jun-2014 01:27 45K 
[ ]pixj-07-arg.shifts_sorted28-Jun-2014 01:27 34K 
[ ]pixj.prot28-Jun-2014 01:27 41K 
[ ]pixj.shifts28-Jun-2014 01:27 41K 
[ ]pixj.tab28-Jun-2014 01:27 24K 
[ ]pixj.tab_old28-Jun-2014 01:27 24K 
[ ]pixj_bb.pipp28-Jun-2014 01:27 28K 
[ ]pixj_blast_align_syb_gaf.asn28-Jun-2014 01:28 2.9K 
[ ]pixj_pg.tab28-Jun-2014 01:27 25K 
[ ]pixj_pvb_shifts28-Jun-2014 01:27 2.1K 
[ ]pixj_pvb_shifts.sort28-Jun-2014 01:27 2.1K 
[ ]pvb_ass.col28-Jun-2014 01:27 868  
[ ]seq28-Jun-2014 01:27 1.1K 
[ ]seq.pine28-Jun-2014 01:27 341  
[ ]seq.talos28-Jun-2014 01:27 244  
[TXT]seq.txt28-Jun-2014 01:28 1.0K 
[ ]seq.xplor28-Jun-2014 01:27 684  
[TXT]seq_bmrb.txt28-Jun-2014 01:27 180  
[TXT]seq_one_line.txt28-Jun-2014 01:27 171  
[TXT]seq_pine_1letter.txt28-Jun-2014 01:27 341  
[DIR]strip_pb/28-Jun-2014 01:27 -  
[DIR]strip_pb_all/28-Jun-2014 01:28 -  
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