Good morning Simon,
Easy enough, though I did have to load a project to get the error. The first traceback is that shiftx is not present (or is in the ccpn distribution but somehow not in the path). The final error looks like it may be a case sensitive thing; I have Cyana_SS4.json but not CYANA_SS4.json at that location.
Cheers,
Andrew
>>> Missing shiftx which is a dep for shiftx
Exception in Tkinter callback
Traceback (most recent call last):
File "/usr/local/ccpnmr/python2.7/lib/python2.7/lib-tk/Tkinter.py", line 1532, in __call__
return self.func(*args)
File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/analysis/AnalysisPopup.py", line 2179, in setupCyanaCalculation
setupCyanaCalculationDialogue(self.argumentServer)
File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/analysis/macros/MultiStructure.py", line 43, in setupCyanaCalculationDialogue
intIo.setupCyana2CcpnDialogue(argServer, protocolName='CYANA_SS4',
File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/integrator/core/Io.py", line 1135, in setupCyana2CcpnDialogue
masterRun=masterRun)
File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/integrator/core/Io.py", line 1236, in setupSingleDialogue
masterRun=masterRun)
File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/integrator/core/Io.py", line 569, in initRunDialogue
nmrCalcRun=nmrCalcRun)
File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/integrator/core/Io.py", line 621, in setupRunDialogue
entryProtocol = getWmsInteractive(argServer, protocolName=protocolName)
File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/integrator/core/Io.py", line 587, in getWmsInteractive
entryProtocol = loadProtocol(project, jsonFile)
File "/usr/local/ccpnmr/ccpnmr2.4/python/ccpnmr/integrator/core/Io.py", line 346, in loadProtocol
jsonObject = json.load(open(jsonFile))
IOError: [Errno 2] No such file or directory: '/usr/local/ccpnmr/ccpnmr2.4/data/ccpnmr/integrator/CYANA_SS4.json'
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C. Andrew Fowler, Ph.D. | University of Iowa
Associate Director | B291 CBRB, 500 Newton Rd.
CCOM NMR Facility | Iowa City, IA 52242
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From: "CcpNmr software mailing list <[log in to unmask]<mailto:[log in to unmask]>>" <[log in to unmask]<mailto:[log in to unmask]>> on behalf of "Skinner, Simon P. (Dr.)" <[log in to unmask]<mailto:[log in to unmask]>>
Reply-To: "CcpNmr software mailing list <[log in to unmask]<mailto:[log in to unmask]>>" <[log in to unmask]<mailto:[log in to unmask]>>
Date: Tuesday, March 15, 2016 at 3:20 AM
To: "CcpNmr software mailing list <[log in to unmask]<mailto:[log in to unmask]>>" <[log in to unmask]<mailto:[log in to unmask]>>
Subject: Re: FormatConverter output and CYANA
Dear Gabriel, Andrew,
Could you send the messsage/traceback in the terminal when Run Cyana Calculation crashes so I can look into it?
Best,
Simon
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Department of Molecular and Cell Biology,
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On 24 Feb 2016, at 08:25, Gabriel Wagner <[log in to unmask]<mailto:[log in to unmask]>> wrote:
In older versions I had the same problem with "M:Structure:Cyana:Run CYANA calculation", with the manual export I can reproduce the problem.
Would be great if this gets fixed.
Anyways, thanks a lot to the CCPNMR team for the great support!
regards,
Gabriel
Gesendet: Dienstag, 23. Februar 2016 um 22:42 Uhr
Von: "Fowler, Andrew" <[log in to unmask]<mailto:[log in to unmask]>>
An: [log in to unmask]<mailto:[log in to unmask]>
Betreff: FormatConverter output and CYANA
Let me preface this by saying that I’m exporting chemical shifts and NOESY peaklists via FormatConverter and then running CYANA manually. I’m not sure if this applies to running from M:Structure:Cyana:Run CYANA calculation or not. The latter crashes on my system.
When I use FormatConverter to export assigned chemical shifts into XEASY/CYANA format (to use as a .prot file in CYANA), the ring delta and epsilon carbon shifts for Phe and Tyr get exported such that some are CD1 and some are CD2, same for CE1 and CE2. This may or may not reflect how they’re assigned in Analysis since a collaborator is doing that. In all cases, there is a single carbon and proton assignment at each position, and the proton correctly gets assigned as QD or QE.
The feature request is to add a check and if the carbon shifts assigned within an aromatic ring are CD2 and/or CE2, please export them as CD1 and CE1 instead. If CYANA sees 999.000 as the CD1 shift, it ignores the value in CD2 and assumes that residue has no carbon assignment. The same is true for CE1 and CE2. Then, during the calculation it doesn’t actually assign any NOESY peaks at that position because there’s no assigned proton/carbon pair within tolerances. Obviously, in the extremely rare case that someone has different assignments for CD1 and CD2 they should both be exported separately.
It took me a bit of sleuthing to figure this out, but we were getting a large number of unassigned aromatic NOE crosspeaks in our calculations that looked like they should be assignable. When I manually edited the .prot file so that the aromatic carbon assignments that were in CD2/CE2 were swapped to CD1/CE1, most of those crosspeaks now have assignments, and the the total number of unassigned peaks dropped by ~2/3.
Cheers,
Andrew
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