Hey Brian,
Try attached chemShiftsIO.py… so replace the original in ccp/format/shiftx/. Let us know if it works, we’ll check it in.
Wim
On 16 Mar 2015, at 10:53, Brian Smith <[log in to unmask]> wrote:
> Hi,
>
> I'm trying to read the output from SHIFTX2 web server into a project (I've tried empty, and already populated).
>
> The files look like
>
> BACKBONE ATOMS
> Num RES CA CB CO N H HA
> 14 P 63.5624 32.1090 175.9337 **** **** 4.4734
> 15 R 55.6609 31.3586 175.4507 118.2871 7.7702 4.3459
> 16 K 55.2252 34.6261 175.5421 125.3618 8.7211 4.5907
>
> etc.
>
> Initially I just got a dialog saying that importing the file had failed. I made the guess that
>
> ccp/format/shiftx/chemShiftsIO.py line 131
>
> if cols[0].count('NUM'):
>
> Is case sensitive so fixed Num to NUM. Now I get the traceback below, which I suspect is an issue with handling the "****" empty shift placeholders since the first three shifts are imported.
>
> Incidentally I was able to read in the webserver output with the NMRStar format - although only after adding the Star wrappers harvested from
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCPNMR;87fbe4c2.1410
> reproduced at the end of this email.
>
> Traceback:
> ERROR in ccp.nmr.Nmr.Shift.__init__
> Exception in Tkinter callback
> Traceback (most recent call last):
> File "/usr/local/lib/python2.7/lib-tk/Tkinter.py", line 1410, in __call__
> return self.func(*args)
> File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/format/gui/ImportExportFormatP
> opup.py", line 981, in ok
> if (not self.apply()):
> File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/format/gui/ImportExportFormatP
> opup.py", line 994, in apply
> returnValue = self.importExportFile(self.component) # If none, will do all c
> omponents
> File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/format/gui/ImportExportFormatP
> opup.py", line 801, in importExportFile
> returnValue = rwFunc(*addArgs,**addKeywds)
> File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/format/converters/DataFormat.p
> y", line 1806, in readShifts
> return self.readMeasurements(*args, **keywds)
> File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/format/converters/DataFormat.p
> y", line 2044, in readMeasurements
> self.setMeasurements()
> File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/format/converters/DataFormat.p
> y", line 5345, in setShifts
> self.setSingleResonanceMeasurementsGeneric()
> File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/format/converters/DataFormat.p
> y", line 5169, in setSingleResonanceMeasurementsGeneric
> self.measurement = self.createMeasurement(resonance,self.rawMeasurement)
> File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/format/converters/DataFormat.p
> y", line 8071, in createShift
> self.createSingleResonanceMeasurement(resonance,rawMeasurement)
> File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/format/converters/DataFormat.p
> y", line 8050, in createSingleResonanceMeasurement
> return self.ApiMeasurement(self.measurementList, value = rawMeasurement.valu
> e, resonance = resonance, **keywds)
> File "/usr/local/ccpnmr/ccpnmr2.4/python/ccp/api/nmr/Nmr.py", line 105944, in
> __init__
> func(self, value)
> File "/usr/local/ccpnmr/ccpnmr2.4/python/ccp/api/nmr/Nmr.py", line 5148, in se
> tValue
> + ": %s" % (value,)
> ApiError: ccp.nmr.Nmr.Shift.setValue:
> memops.Implementation.Float input is not of a valid type: None
>
> NMRStar header and footer:
>
>
> 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
> ....SHIFTX2 output here......
> stop_
> save_
>
>
>
> Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
> Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
> College of Medical, Veterinary & Life Sciences,
> Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
> Tel: 0141 330 5167/6459/3089
> ----------------------------------------------------------------------
> The University of Glasgow, charity number SC004401
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