Hi John
"puts $saRemarks" after the call to createShiftAssignments showed that the
peak assignment file amino acid codes needed to be changed from one letter
to three. After doing that I got no output from "puts $saRemarks" after the
call to createShiftAssignments.
I added a "puts $peakRemarks" after the call to process3dCnmrDrawPeakTable
and got {Created 444 peaks from file ./pipesybcnsy.tab}
"puts $peakRemarks" after standard3dInitMatch gave
{DropShiftAssignmentsInShiftRange: Dropped 0 shiftAssigns with fromProton in
range 9.010000 .. 99999.000000 ppm} {DropShiftAssignmentsInShiftRange:
Dropped 0 shiftAssigns with fromProton in range -99999.000000 .. -0.010000
ppm} {DropShiftAssignmentsInShiftRange: Dropped 0 shiftAssigns with toProton
in range 9.000000 .. 99999.000000 ppm} {DropShiftAssignmentsInShiftRange:
Dropped 0 shiftAssigns with toProton in range -99999.000000 .. -0.010000
ppm} {Consolidated 0 pairs of identical stereopartners:}
{recordStereoPartnersForShiftAssignments: 0 shiftAssignments had partners}
{0 of 0 stereospecific shiftAssignments were expanded by
expandStereospecificShiftAssignments}
{recordToFromPartnersForShiftAssignments: 0 shiftAssignments had partners}
{recordToFromPartnersForShiftAssignments: 0 shiftAssignments had no
partners} {Found 0 methyl shift assignments.}
and puts $errorInfo at the end of the script gave
Neither -pot nor -shiftAssignments defined in call to
recordUnfoldedPositions
while executing
"error "Neither -pot nor -shiftAssignments defined in call to
recordUnfoldedPositions""
(procedure "recordUnfoldedPositions" line 7)
invoked from within
"recordUnfoldedPositions -shiftAssignments [concat
$fromSAs $toSAs] -fromProtonSpectralRange $fromProtonRange
..."
(procedure "match3d" line 79)
invoked from within
"match3d -peakList [$pot peaks] -fromProtonTolerancePPM
$fromProtonBroadTol -fromProtonSpectralRangePPM $fromProtonRange
-fromHeavyatomTolerancePP..."
(procedure "standard3dInitMatch" line 67)
invoked from within
"standard3dInitMatch -pot $noe \
-fromProtonSpectralRangePPM [list 9.01 -0.01] \
-fromHeavyatomSpectralRangePPM [list 77.6 7.83] \
-toProt..."
Finally the terminal output indicated
Expected integer but got ""
Can't read "shifts": no such variable
Can't read "shifts": no such variable
Neither -pot nor -shiftAssignments defined in call to
recordUnfoldedPositions
What should I do to avoid the above errors?
I don't have any folded peaks is there a way to tell that to initMatch3dC?
Thanks,
Jeff
_____
From: John Kuszewski [mailto:[email protected]]
Sent: Thursday, February 12, 2009 12:07 AM
To: Jeff Ellena
Cc: xplor-nih at nmr.cit.nih.gov
Subject: Re: [Xplor-nih] pasd
On Feb 11, 2009, at 9:05 AM, Jeff Ellena wrote:
I also get output that I don't understand following
set noe [create_MarvinNOEPotential marv]
Does the following xplor output indicate that there is be a problem with
setting $noe?
TCL>set noe [create_MarvinNOEPotential marv]
_b06baf0000000000_p_rc_DerivedPotTMarvinNOEPotential_t
No, that's just the weird way SWIG returns a pointer value. It's fine.
The error message preceeding the premature exit of initMatch3dC.tcl is:
Neither -pot nor -shiftAssignments defined in call to
recordUnfoldedPositions
Sorry for the unhelpful error message. The most likely cause is a problem
in your readNMRSTARShiftTable or your createShiftAssignments calls, such
that no shiftAssignments were produced.
Try inserting a "puts $saRemarks" after the call to createShiftAssignments
to see what's going on.
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