This sounds like it might be worth me trying to debug that data file, but
I guess it's so huge that it would mean DVD (i.e. real mail) transfer
rather than http to get it over here.
The Ansig contours format was changed for Analysis (for one thing to deal
with negative contours the same as positive). So the two are incompatible
and we definitely haven't tried to allow the old contour files to be read
It would be good if we could get to the bottom of this.
On Thu, 15 May 2008, Andrew Fowler wrote:
> First, thanks to Wayne, Patrick, and Justin for suggestions so far.
> pipe2azara deals just fine with a "single" nmrpipe file as input (not sure
> why I thought otherwise, works beautifully). The spectrum will open and
> display contours on-the-fly, albeit too slowly to be useful for any sort of
> scrolling through spectra for assignments. Same is true for ucsf format.
> Presumably pre-calculated contour files will fix this speed issue, but
> that's where a bit of frustration starts to set in...
> If I adjust my contour levels to something reasonable in terms of both S/N
> and number of levels (6 each +/-) and then try to pre-calculate contours in
> this orthogonal (zy) dimension (new contour file button), it runs for a
> minute or so and then dump core with the following output:
> /usr/local/ccpnmr/bin/analysis: line 8: 768 Segmentation fault
> /sw/bin/python -i -O
> $CCPNMR_TOP_DIR/ccpnmr1.0/python/ccpnmr/analysis/AnalysisGui.py $1 $2 $3 $4
> The message prior to that is that the Azara format spectrum successfully
> opened. For what it's worth, I'm working in a separate project trying to
> sort this out, so this is the only spectrum and only window open.
> Before core gets dumped, a ~14 MB file is created in the project's
> contourStore directory. I've tried to manually add this file, and get
> another core dump trying to read it.
> Now that I have the data in Azara format, I've also tried using the old
> "contours" program. This goes through 50 chunks or so as expected and
> creates a reasonable sized file (a bit under 3 megs after I adjust the
> thresholds up, a scaling factor vs. analysis?). If I try to add this to my
> project, I get a "magic number invalid" error. Do Analyis and Azara use
> different formats for storing contour data?
> Summary - block data is a major improvement, but I still can't contour
> except in the normal (xy) dimension. Any further suggestions?
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