Hi All,
I used SHIFTX2 to predict chemical shifts from a pdb file but am unable to import the chemical shifts into a CCPN Analysis project using FormatConverter. Do you know what might be going wrong? The CS table is in NMR-STAR format.
Best wishes,
Justin
The following text is from my Terminal window:
###############################################
# FormatConverter: executing readMeasurements #
###############################################
#########################################
# FormatConverter: executing readShifts #
#########################################
save_shifts
_Saveframe_category assigned_chemical_shifts
loop_
_Atom_shift_assign_ID
_Residue_seq_code
_Residue_label
_Atom_name
_Chem_shift_value
_Chem_shift_value_error
_Chem_shift_ambiguity_code
1 1 VAL C 177.3826 . 1
2 1 VAL CA 64.3535 . 1
3 1 VAL CB 31.3190 . 1
4 1 VAL H 8.1472 . 1
5 1 VAL HA 4.0662 . 1
6 1 VAL N 120.3660 . 1
7 2 GLU C 178.8181 . 1
8 2 GLU CA 58.6220 . 1
9 2 GLU CB 28.5258 . 1
10 2 GLU H 8.5901 . 1
11 2 GLU HA 4.1380 . 1
12 2 GLU N 120.4838 . 1
13 3 GLU C 179.2560 . 1
14 3 GLU CA 59.2584 . 1
15 3 GLU CB 28.7622 . 1
16 3 GLU H 7.9641 . 1
17 3 GLU HA 4.0435 . 1
18 3 GLU N 119.7912 . 1
19 4 SER C 176.5196 . 1
20 4 SER CA 61.0410 . 1
21 4 SER CB 62.1084 . 1
22 4 SER H 7.7419 . 1
23 4 SER HA 4.2643 . 1
24 4 SER N 114.5034 . 1
25 5 ARG C 178.0390 . 1
26 5 ARG CA 58.7799 . 1
27 5 ARG CB 29.2997 . 1
28 5 ARG H 8.4219 . 1
29 5 ARG HA 4.0703 . 1
30 5 ARG N 120.8807 . 1
31 6 ALA C 179.2660 . 1
32 6 ALA CA 53.2897 . 1
33 6 ALA CB 18.3364 . 1
34 6 ALA H 7.7592 . 1
35 6 ALA HA 4.2962 . 1
36 6 ALA N 118.7074 . 1
37 7 ARG C 177.2189 . 1
38 7 ARG CA 57.0518 . 1
39 7 ARG CB 29.0065 . 1
40 7 ARG H 7.9756 . 1
41 7 ARG HA 4.2581 . 1
42 7 ARG N 116.4178 . 1
43 8 LEU C 179.4859 . 1
44 8 LEU CA 56.2260 . 1
45 8 LEU CB 41.1045 . 1
46 8 LEU H 7.6483 . 1
47 8 LEU HA 4.2026 . 1
48 8 LEU N 119.1890 . 1
49 9 THR C 176.4333 . 1
50 9 THR CA 65.9342 . 1
51 9 THR CB 67.3042 . 1
52 9 THR H 7.6264 . 1
53 9 THR HA 3.9044 . 1
54 9 THR N 115.4369 . 1
55 10 LYS C 179.4066 . 1
56 10 LYS CA 59.4739 . 1
57 10 LYS CB 30.8714 . 1
58 10 LYS H 7.5367 . 1
59 10 LYS HA 4.0112 . 1
60 10 LYS N 120.1839 . 1
61 11 LEU C 179.6181 . 1
62 11 LEU CA 57.3365 . 1
63 11 LEU CB 40.2415 . 1
64 11 LEU H 7.6872 . 1
65 11 LEU HA 4.0857 . 1
66 11 LEU N 119.7803 . 1
67 12 GLN C 178.1336 . 1
68 12 GLN CA 58.4539 . 1
69 12 GLN CB 27.6027 . 1
70 12 GLN H 7.9877 . 1
71 12 GLN HA 3.9833 . 1
72 12 GLN N 118.4549 . 1
73 13 GLU C 178.8668 . 1
74 13 GLU CA 58.1879 . 1
75 13 GLU CB 28.7954 . 1
76 13 GLU H 8.1447 . 1
77 13 GLU HA 4.1257 . 1
78 13 GLU N 117.3056 . 1
79 14 ASP C 179.0225 . 1
80 14 ASP CA 56.9044 . 1
81 14 ASP CB 39.7298 . 1
82 14 ASP H 8.4769 . 1
83 14 ASP HA 4.4302 . 1
84 14 ASP N 119.9720 . 1
85 15 LEU C 179.0875 . 1
86 15 LEU CA 58.7316 . 1
87 15 LEU CB 39.3153 . 1
88 15 LEU H 8.7381 . 1
89 15 LEU HA 4.1317 . 1
90 15 LEU N 120.4673 . 1
91 16 PRO C 179.1907 . 1
92 16 PRO CA 65.2518 . 1
93 16 PRO CB 30.2944 . 1
94 16 PRO HA 4.2322 . 1
95 17 GLU C 179.2725 . 1
96 17 GLU CA 58.3331 . 1
97 17 GLU CB 29.2482 . 1
98 17 GLU H 7.5859 . 1
99 17 GLU HA 4.1486 . 1
100 17 GLU N 117.3913 . 1
101 18 GLN C 178.0698 . 1
102 18 GLN CA 57.7701 . 1
103 18 GLN CB 27.6251 . 1
104 18 GLN H 8.1286 . 1
105 18 GLN HA 4.1173 . 1
106 18 GLN N 118.5759 . 1
107 19 LEU C 178.9603 . 1
108 19 LEU CA 56.3617 . 1
109 19 LEU CB 40.5998 . 1
110 19 LEU H 7.9027 . 1
111 19 LEU HA 4.1941 . 1
112 19 LEU N 118.9842 . 1
113 20 THR C 176.2360 . 1
114 20 THR CA 65.3119 . 1
115 20 THR CB 67.9979 . 1
116 20 THR H 7.6339 . 1
117 20 THR HA 4.0806 . 1
118 20 THR N 116.3740 . 1
119 21 GLU C 177.6968 . 1
120 21 GLU CA 56.6165 . 1
121 21 GLU CB 29.3514 . 1
122 21 GLU H 7.6501 . 1
123 21 GLU HA 4.1621 . 1
124 21 GLU N 121.0930 . 1
stop_save_
Warning: fixing input file to be correct NMR-STAR. This might not work.
Python nmrStar reader courtesy of Jurgen Doreleijers (BMRB) - with modifications added.
Parsing STAR file: /Users/jyeoman/Documents/Dynamics Post-Doc/Data/SHIFTX2/1414521348.h2_wt_A.pdb.cs
Warning: Found no 'data_title' string in file's text.
Warning: Your file is not valid NMR-STAR - to attempt reading
Warning: this file a data_title tag was added automatically.
WARNING: EOF in tagtable, must be a CIF file
ERROR: not correct number of tag values read
Read [869] tag(s) that is:
[124] row(s) complete and [1] tag value(s) in last row that is incomplete.
Tag names of this table are:
['_Atom_shift_assign_ID', '_Residue_seq_code', '_Residue_label', '_Atom_name', '_Chem_shift_value', '_Chem_shift_value_error', '_Chem_shift_ambiguity_code']
1 1 VAL C 177.3826 . 1
-----------------------------------------------
2 1 VAL CA 64.3535 . 1
-----------------------------------------------
3 1 VAL CB 31.3190 . 1
-----------------------------------------------
4 1 VAL H 8.1472 . 1
-----------------------------------------------
5 1 VAL HA 4.0662 . 1
-----------------------------------------------
6 1 VAL N 120.3660 . 1
-----------------------------------------------
7 2 GLU C 178.8181 . 1
-----------------------------------------------
8 2 GLU CA 58.6220 . 1
-----------------------------------------------
9 2 GLU CB 28.5258 . 1
-----------------------------------------------
10 2 GLU H 8.5901 . 1
-----------------------------------------------
11 2 GLU HA 4.1380 . 1
-----------------------------------------------
12 2 GLU N 120.4838 . 1
-----------------------------------------------
13 3 GLU C 179.2560 . 1
-----------------------------------------------
14 3 GLU CA 59.2584 . 1
-----------------------------------------------
15 3 GLU CB 28.7622 . 1
-----------------------------------------------
16 3 GLU H 7.9641 . 1
-----------------------------------------------
17 3 GLU HA 4.0435 . 1
-----------------------------------------------
18 3 GLU N 119.7912 . 1
-----------------------------------------------
19 4 SER C 176.5196 . 1
-----------------------------------------------
20 4 SER CA 61.0410 . 1
-----------------------------------------------
21 4 SER CB 62.1084 . 1
-----------------------------------------------
22 4 SER H 7.7419 . 1
-----------------------------------------------
23 4 SER HA 4.2643 . 1
-----------------------------------------------
24 4 SER N 114.5034 . 1
-----------------------------------------------
25 5 ARG C 178.0390 . 1
-----------------------------------------------
26 5 ARG CA 58.7799 . 1
-----------------------------------------------
27 5 ARG CB 29.2997 . 1
-----------------------------------------------
28 5 ARG H 8.4219 . 1
-----------------------------------------------
29 5 ARG HA 4.0703 . 1
-----------------------------------------------
30 5 ARG N 120.8807 . 1
-----------------------------------------------
31 6 ALA C 179.2660 . 1
-----------------------------------------------
32 6 ALA CA 53.2897 . 1
-----------------------------------------------
33 6 ALA CB 18.3364 . 1
-----------------------------------------------
34 6 ALA H 7.7592 . 1
-----------------------------------------------
35 6 ALA HA 4.2962 . 1
-----------------------------------------------
36 6 ALA N 118.7074 . 1
-----------------------------------------------
37 7 ARG C 177.2189 . 1
-----------------------------------------------
38 7 ARG CA 57.0518 . 1
-----------------------------------------------
39 7 ARG CB 29.0065 . 1
-----------------------------------------------
40 7 ARG H 7.9756 . 1
-----------------------------------------------
41 7 ARG HA 4.2581 . 1
-----------------------------------------------
42 7 ARG N 116.4178 . 1
-----------------------------------------------
43 8 LEU C 179.4859 . 1
-----------------------------------------------
44 8 LEU CA 56.2260 . 1
-----------------------------------------------
45 8 LEU CB 41.1045 . 1
-----------------------------------------------
46 8 LEU H 7.6483 . 1
-----------------------------------------------
47 8 LEU HA 4.2026 . 1
-----------------------------------------------
48 8 LEU N 119.1890 . 1
-----------------------------------------------
49 9 THR C 176.4333 . 1
-----------------------------------------------
50 9 THR CA 65.9342 . 1
-----------------------------------------------
51 9 THR CB 67.3042 . 1
-----------------------------------------------
52 9 THR H 7.6264 . 1
-----------------------------------------------
53 9 THR HA 3.9044 . 1
-----------------------------------------------
54 9 THR N 115.4369 . 1
-----------------------------------------------
55 10 LYS C 179.4066 . 1
-----------------------------------------------
56 10 LYS CA 59.4739 . 1
-----------------------------------------------
57 10 LYS CB 30.8714 . 1
-----------------------------------------------
58 10 LYS H 7.5367 . 1
-----------------------------------------------
59 10 LYS HA 4.0112 . 1
-----------------------------------------------
60 10 LYS N 120.1839 . 1
-----------------------------------------------
61 11 LEU C 179.6181 . 1
-----------------------------------------------
62 11 LEU CA 57.3365 . 1
-----------------------------------------------
63 11 LEU CB 40.2415 . 1
-----------------------------------------------
64 11 LEU H 7.6872 . 1
-----------------------------------------------
65 11 LEU HA 4.0857 . 1
-----------------------------------------------
66 11 LEU N 119.7803 . 1
-----------------------------------------------
67 12 GLN C 178.1336 . 1
-----------------------------------------------
68 12 GLN CA 58.4539 . 1
-----------------------------------------------
69 12 GLN CB 27.6027 . 1
-----------------------------------------------
70 12 GLN H 7.9877 . 1
-----------------------------------------------
71 12 GLN HA 3.9833 . 1
-----------------------------------------------
72 12 GLN N 118.4549 . 1
-----------------------------------------------
73 13 GLU C 178.8668 . 1
-----------------------------------------------
74 13 GLU CA 58.1879 . 1
-----------------------------------------------
75 13 GLU CB 28.7954 . 1
-----------------------------------------------
76 13 GLU H 8.1447 . 1
-----------------------------------------------
77 13 GLU HA 4.1257 . 1
-----------------------------------------------
78 13 GLU N 117.3056 . 1
-----------------------------------------------
79 14 ASP C 179.0225 . 1
-----------------------------------------------
80 14 ASP CA 56.9044 . 1
-----------------------------------------------
81 14 ASP CB 39.7298 . 1
-----------------------------------------------
82 14 ASP H 8.4769 . 1
-----------------------------------------------
83 14 ASP HA 4.4302 . 1
-----------------------------------------------
84 14 ASP N 119.9720 . 1
-----------------------------------------------
85 15 LEU C 179.0875 . 1
-----------------------------------------------
86 15 LEU CA 58.7316 . 1
-----------------------------------------------
87 15 LEU CB 39.3153 . 1
-----------------------------------------------
88 15 LEU H 8.7381 . 1
-----------------------------------------------
89 15 LEU HA 4.1317 . 1
-----------------------------------------------
90 15 LEU N 120.4673 . 1
-----------------------------------------------
91 16 PRO C 179.1907 . 1
-----------------------------------------------
92 16 PRO CA 65.2518 . 1
-----------------------------------------------
93 16 PRO CB 30.2944 . 1
-----------------------------------------------
94 16 PRO HA 4.2322 . 1
-----------------------------------------------
95 17 GLU C 179.2725 . 1
-----------------------------------------------
96 17 GLU CA 58.3331 . 1
-----------------------------------------------
97 17 GLU CB 29.2482 . 1
-----------------------------------------------
98 17 GLU H 7.5859 . 1
-----------------------------------------------
99 17 GLU HA 4.1486 . 1
-----------------------------------------------
100 17 GLU N 117.3913 . 1
-----------------------------------------------
101 18 GLN C 178.0698 . 1
-----------------------------------------------
102 18 GLN CA 57.7701 . 1
-----------------------------------------------
103 18 GLN CB 27.6251 . 1
-----------------------------------------------
104 18 GLN H 8.1286 . 1
-----------------------------------------------
105 18 GLN HA 4.1173 . 1
-----------------------------------------------
106 18 GLN N 118.5759 . 1
-----------------------------------------------
107 19 LEU C 178.9603 . 1
-----------------------------------------------
108 19 LEU CA 56.3617 . 1
-----------------------------------------------
109 19 LEU CB 40.5998 . 1
-----------------------------------------------
110 19 LEU H 7.9027 . 1
-----------------------------------------------
111 19 LEU HA 4.1941 . 1
-----------------------------------------------
112 19 LEU N 118.9842 . 1
-----------------------------------------------
113 20 THR C 176.2360 . 1
-----------------------------------------------
114 20 THR CA 65.3119 . 1
-----------------------------------------------
115 20 THR CB 67.9979 . 1
-----------------------------------------------
116 20 THR H 7.6339 . 1
-----------------------------------------------
117 20 THR HA 4.0806 . 1
-----------------------------------------------
118 20 THR N 116.3740 . 1
-----------------------------------------------
119 21 GLU C 177.6968 . 1
-----------------------------------------------
120 21 GLU CA 56.6165 . 1
-----------------------------------------------
121 21 GLU CB 29.3514 . 1
-----------------------------------------------
122 21 GLU H 7.6501 . 1
-----------------------------------------------
123 21 GLU HA 4.1621 . 1
-----------------------------------------------
124 21 GLU N 121.0930 . 1
-----------------------------------------------
Exception in Tkinter callback
Traceback (most recent call last):
File "/Applications/ccpnmr/python2.6/lib/python2.6/lib-tk/Tkinter.py", line 1410, in __call__
return self.func(*args)
File "/Applications/ccpnmr/ccpnmr2.3/python/ccpnmr/format/gui/ImportExportFormatPopup.py", line 981, in ok
if (not self.apply()):
File "/Applications/ccpnmr/ccpnmr2.3/python/ccpnmr/format/gui/ImportExportFormatPopup.py", line 994, in apply
returnValue = self.importExportFile(self.component) # If none, will do all components
File "/Applications/ccpnmr/ccpnmr2.3/python/ccpnmr/format/gui/ImportExportFormatPopup.py", line 801, in importExportFile
returnValue = rwFunc(*addArgs,**addKeywds)
File "/Applications/ccpnmr/ccpnmr2.3/python/ccpnmr/format/converters/DataFormat.py", line 1792, in readShifts
return self.readMeasurements(*args, **keywds)
File "/Applications/ccpnmr/ccpnmr2.3/python/ccpnmr/format/converters/DataFormat.py", line 1930, in readMeasurements
self.getMeasurements()
File "/Applications/ccpnmr/ccpnmr2.3/python/ccpnmr/format/converters/NmrStarFormat.py", line 338, in getMeasurements
self.nmrStarFile.read()
File "/Applications/ccpnmr/ccpnmr2.3/python/ccp/format/nmrStar/chemShiftsIO.py", line 115, in read
self.readComponent(verbose = verbose)
File "/Applications/ccpnmr/ccpnmr2.3/python/ccp/format/nmrStar/generalIO.py", line 1786, in readComponent
self.readGeneric(verbose = verbose)
File "/Applications/ccpnmr/ccpnmr2.3/python/ccp/format/nmrStar/generalIO.py", line 1817, in readGeneric
if origNmrStarFile.read(text = self.text):
File "/Applications/ccpnmr/ccpnmr2.3/python/ccp/format/nmrStar/bmrb/File.py", line 138, in read
if self.parse( text=text, strip_comments=strip_comments, nmrView_type = nmrView_type):
File "/Applications/ccpnmr/ccpnmr2.3/python/ccp/format/nmrStar/bmrb/File.py", line 303, in parse
pos = tt.parse( text=text, pos=pos )
File "/Applications/ccpnmr/ccpnmr2.3/python/ccp/format/nmrStar/bmrb/TagTable.py", line 414, in parse
text, pos, pos_end): ## will set title too
File "/Applications/ccpnmr/ccpnmr2.3/python/ccp/format/nmrStar/bmrb/TagTable.py", line 598, in _tagtable_loop_values_parse
print self.tagvalues[yyy][xxx],
IndexError: list index out of range
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