Are the stop_ and save_ at the end connected? They should be separated by a newline.
On 28 Oct 2014, at 20:29, Justin Yeoman <[log in to unmask]> wrote:
> 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
---------------------------------------------------------------------------------------
Prof. Dr. Wim Vranken
[log in to unmask] Tel: +32 (0)2 6291025 (VUB)
+32 (0)2 6505943 (IB^2)
Building E, 5th Floor, E5.05, Pleinlaan 2
1050 Brussels, Belgium
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Vice-director, http://ibsquare.be/
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