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

	Name	Last modified	Size	Description
	Parent Directory		-
	000-readme	28-Jun-2014 01:27	662
	2O9C.pdb	28-Jun-2014 01:27	298K
	2nd_inCS.tab	28-Jun-2014 01:27	41K
	13C_NMR_heme.pdf	28-Jun-2014 01:27	1.0M
	blast.txt	28-Jun-2014 01:27	1.7K
	bmrb2talos	28-Jun-2014 01:27	3.3K
	bmrb2talos.awk	28-Jun-2014 01:27	1.6K
	cbca	28-Jun-2014 01:27	132K
	cco	28-Jun-2014 01:27	153K
	ccpn/	28-Jun-2014 01:27	-
	clustal.txt	28-Jun-2014 01:27	1.9K
	diff_pr_pfr.tcl	28-Jun-2014 01:28	5.5K
	diff_pr_pfr_hn.tcl	28-Jun-2014 01:27	4.5K
	getseq.tcl	28-Jun-2014 01:27	1.7K
	hbha	28-Jun-2014 01:27	127K
	hcco	28-Jun-2014 01:27	186K
	hncacb	28-Jun-2014 01:27	187K
	hnco	28-Jun-2014 01:27	70K
	hnco.sort	28-Jun-2014 01:27	58K
	hnco_no_conf	28-Jun-2014 01:27	58K
	hnco_wrong	28-Jun-2014 01:27	70K
	merge_pipp.tcl	28-Jun-2014 01:27	8.3K
	methines	28-Jun-2014 01:27	88
	model.pdb	28-Jun-2014 01:27	80K
	model.pse	28-Jun-2014 01:27	307K
	model_h.pdb	28-Jun-2014 01:28	182K
	model_project.pdb	28-Jun-2014 01:27	176K
	pipe2pipp.tcl	28-Jun-2014 01:27	5.9K
	pipe2pipp_sc.tcl	28-Jun-2014 01:27	8.0K
	pipp2col.tcl	28-Jun-2014 01:27	3.3K
	pipp2prot.tcl	28-Jun-2014 01:27	4.7K
	pipp2talos.tcl	28-Jun-2014 01:27	3.3K
	pixj-01-ccc.shifts	28-Jun-2014 01:27	46K
	pixj-01-ccc.shifts-differences	28-Jun-2014 01:27	7.4K
	pixj-01-ccc.shifts_corrected	28-Jun-2014 01:27	46K
	pixj-01-ccc.shifts_corrected.col	28-Jun-2014 01:27	40K
	pixj-01-ccc.shifts_corrected.sort	28-Jun-2014 01:28	41K
	pixj-01-ccc.shifts_corrected.sort2	28-Jun-2014 01:27	41K
	pixj-01-ccc.shifts_corrected.sortwrong	28-Jun-2014 01:27	41K
	pixj-02.shifts	28-Jun-2014 01:28	46K
	pixj-02.shifts_col	28-Jun-2014 01:27	42K
	pixj-02.shifts_sort	28-Jun-2014 01:27	42K
	pixj-03.shifts	28-Jun-2014 01:27	49K
	pixj-03.shifts_col	28-Jun-2014 01:27	44K
	pixj-03.shifts_sort	28-Jun-2014 01:27	33K
	pixj-04.shifts	28-Jun-2014 01:27	52K
	pixj-04.shifts-p4	28-Jun-2014 01:27	51K
	pixj-04.shifts_col	28-Jun-2014 01:28	44K
	pixj-04.shifts_sort	28-Jun-2014 01:27	44K
	pixj-05.shifts	28-Jun-2014 01:27	52K
	pixj-05.shifts_col	28-Jun-2014 01:27	44K
	pixj-05.shifts_sorted	28-Jun-2014 01:27	33K
	pixj-06.shifts	28-Jun-2014 01:27	52K
	pixj-06.shifts_col	28-Jun-2014 01:27	45K
	pixj-06.shifts_sort	28-Jun-2014 01:27	45K
	pixj-06.shifts_sorted	28-Jun-2014 01:27	34K
	pixj-07-arg.prot	28-Jun-2014 01:27	46K
	pixj-07-arg.shifts	28-Jun-2014 01:27	52K
	pixj-07-arg.shifts-bak	28-Jun-2014 01:27	52K
	pixj-07-arg.shifts_col	28-Jun-2014 01:27	45K
	pixj-07-arg.shifts_sort	28-Jun-2014 01:27	45K
	pixj-07-arg.shifts_sorted	28-Jun-2014 01:27	34K
	pixj.prot	28-Jun-2014 01:27	41K
	pixj.shifts	28-Jun-2014 01:27	41K
	pixj.tab	28-Jun-2014 01:27	24K
	pixj.tab_old	28-Jun-2014 01:27	24K
	pixj_bb.pipp	28-Jun-2014 01:27	28K
	pixj_blast_align_syb_gaf.asn	28-Jun-2014 01:28	2.9K
	pixj_pg.tab	28-Jun-2014 01:27	25K
	pixj_pvb_shifts	28-Jun-2014 01:27	2.1K
	pixj_pvb_shifts.sort	28-Jun-2014 01:27	2.1K
	pvb_ass.col	28-Jun-2014 01:27	868
	seq	28-Jun-2014 01:27	1.1K
	seq.pine	28-Jun-2014 01:27	341
	seq.talos	28-Jun-2014 01:27	244
	seq.txt	28-Jun-2014 01:28	1.0K
	seq.xplor	28-Jun-2014 01:27	684
	seq_bmrb.txt	28-Jun-2014 01:27	180
	seq_one_line.txt	28-Jun-2014 01:27	171
	seq_pine_1letter.txt	28-Jun-2014 01:27	341
	strip_pb/	28-Jun-2014 01:27	-
	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