Hi all,
Concerning this thread, we got a solution figured out in the end - see
below for the relevant info.
Wim
>Hi Baptiste,
>
>Got a possible fix for you - exporting both the XEasy shift list and the
>peak list after unselecting 'Compress names in output' seems to give the
>correct results. The only possible problem (as you noted before) is that
>equivalent atoms are 'split up', as in:
>
>1376 2.361 0.000 HG2 91
>1377 2.361 0.000 HG3 91
>1378 999.000 0.000 QG 91
>
>But because both 1376 and 1377 will be, in this case, referred to in the
>peak list instead of 1378 that shouldn't be a problem (in fact, it's even
>more correct in many ways). I just hope that CYANA can handle it!
>
>Anyway! The problem is that unselecting the 'Compress names in output'
>option wasn't working for the XEasy peak list, so that is fixable in the
>following way:
>
>edit the file:
>
>python/ccpnmr/format/converters/XEasyFormat.py
>
>in the function:
>
> def createMeasurementFileFormatSpecific(self):
>
>change the lines:
>
> if self.compressResonances:
> self.atomSerialDict = {}
>
>to:
>
> self.atomSerialDict = {}
>
>
>and at the bottom of function:
>
> def setChemShiftFileValue(self):
>
>change the lines:
>
> if self.compressResonances:
> self.atomSerialDict[(self.chain,self.residue.seqId,self.atomName)]
> = self.atomSerial
>
>to:
>
> self.atomSerialDict[(self.chain,self.residue.seqId,self.atomName)] =
> self.atomSerial
>
>
>So basically remove the self.compressResonances-dependent if statements.
>The output peak file then has the correct atom serial references, as far
>as I could figure out. I've attached the .peaks/.prot pair so you can give
>them a quick try with CYANA!
>
>Let me know if that works,
>
>Wim
|