Hello,
I'm trying to run pasd/marvin using peak lists from c13 and n15 noesy data
sets exported from cara in capp format (like cvn tutorial) and shift
assignments in Pipp format (also like cvn tutorial). The initMatch3dC.tcl
fails with the following message,
*Attempt to calculate the mean of an empty list
while executing
"error "Attempt to calculate the mean of an empty list""
(procedure "mean" line 4)
invoked from within
"mean $nonZeroDegens"
(procedure "initialPeakAnalysis" line 193)
invoked from within
"initialPeakAnalysis -pot $pot -violCutoff 0.5 -minLikelihood 0.9
-referenceStructureFile $refStructFileName -description "Broad-tolerance
match" ..."
(procedure "standard3dInitMatch" line 151)
invoked from within
"standard3dInitMatch -pot $noe \
-fromProtonSpectralRangePPM [readSpectralRangeFromPippPeakTable
-fileName ./3dc_capp_def.PCK -axis X_AXIS] \
*
And therefore fails to create the 3dc_pass1.shiftAssignments,
3dc_pass1.peaks and 3dc.expections files. The initMatch3dN.tcl script seemed
to work fine as all three 3dn versions of the bold files were created and
seemed to complete running the entire script without any notable errors is
the initMatch3dN.tc.out file. I am hoping you can help me troubleshoot the
problem with the initMatch3dC.tcl script b/c I've had no luck making any
headway. I added the puts $saRemarks line in the initMatch3dC.tcl script
here,
*standard3dInitMatch -pot $noe \
-fromProtonSpectralRangePPM [**readSpectralRangeFromPippPeakT**able
-fileName ./3dc_capp_def.PCK -axis X_AXIS] \
-fromHeavyatomSpectralRangePPM [**readSpectralRangeFromPippPeakT**able
-fileName ./3dc_capp_def.PCK -axis Z_AXIS] \
-toProtonSpectralRangePPM [**readSpectralRangeFromPippPeakT**able
-fileName ./3dc_capp_def.PCK -axis Y_AXIS] \
-basePhase negative \
-fromProtonSolventRange [list 4.6 4.8] \
-exceptionsFileName ./3dc.exceptions \
-peakFileName ./3dc_pass1.peaks \
-shiftAssignmentsFileName ./3dc_pass1.shiftAssignments \
-peakRemarksVariableName peakRemarks \
-saRemarksVariableName saRemarks
puts $saRemarks
*
But the saRemarks don't really help me solve the problem. The problem
doesn't seem to be formating of the 3dc_capp_def.PCK or c13noe.shifts files
as the same formating worked just fine for the 3dn versions. It seems that
all of the "shift assignments make no peak assignments" and that is why I
got the empty list error. I'm not sure if this results from a difference in
chemical shift between the spins and the peaks which is too large to be
resolved by the initMatch3dC.tcl script or if this is some other problem.
Anyhelp would be greatly appreciated.
Thank-you,
Chris Warner
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