Hi Wayne,

Thanks for the input. The final matrix, having extracted the bits that
contain data in the 1H dimensions, is 1616 x 809 x 512 points (block sizes
of 32 x 16 x 8 according to the .spc.par file for what I'm guessing is a
final block size of 4k). I've been converting from Pipe to Azara format for
all spectra going into Analysis for some time now and only tried importing
this as Pipe after getting the error several times, which seems to be
independent of data format.

The final dataset in either format is ~2.7 gigs, as you say much bigger. An
HMQC-NOESY dataset (13C for the other proton) that's half the size in the
indirect proton for a total of ~1.4 gig opened fine.

Slow isn't a problem, but not getting the file open is. I just tried
reconverting to Azara format (letting pipe2azara figure out the block size)
and have the same result. You have confirmed what I figured that it's taking
a random sample to calculate noise for the initial contour threshold and
dying on that for some reason.

Is it possible to either change the block size during conversion (i.e. work
in 16k blocks) or not have Analysis try to calculate noise - maybe force it
to initially display at a very high contour level and then drop it down
manually?

Any suggestions greatly appreciated.

Thanks again,
Andrew


On 1/22/09 1:45 PM, "Wayne Boucher" <[log in to unmask]> wrote:

> Hello,
> 
> This could be a couple of things.  First of all, I should say that that
> bit of the code with the error message is all about doing a random sample
> of the data to try and estimate the noise level of the spectrum.  Since
> it's random it means that if something is going wrong then the exact point
> is likely to differ from attempt to attempt.
> 
> That point (201 390 493) is pretty big.  So just that number implies a
> data file that should be at least 150Mb in size (and probably much
> bigger).  So has the data file been truncated perhaps??  We should
> probably check the data file size against the number of points so we don't
> get this obscure error.
> 
> And I should say that for a large 3D data set like this, NmrPipe format
> will normally not be a good one to use because (at least the examples I've
> seen) it is not blocked, which makes access pretty slow (that might be
> what you are observing), especially in the dimensions other than the
> first.
> 
> Wayne
> 
> On Thu, 22 Jan 2009, Andrew Fowler wrote:
> 
>> I'm trying - unsuccessfully - to import a NOESY-13C-HMQC dataset into an
>> existing project. The data was processed and looks fine in NMRPipe. I am
>> using a fully updated version of Analysis v1. I haven't taken the plunge to
>> v2 yet.
>> 
>> This experiment just does not want to import. I've tried it both as NMRPipe
>> data and converted into Azara format. I select the file in the "open
>> spectrum" dialog, all goes well until what is normally the end where I set
>> the experiment type to H_H[C].NOESY (I've also tried H[C]_H.NOESY). At this
>> point I close the dialog which usually "freezes" for a short time while it
>> loads and displays the data. In this case, however, the dialog immediately
>> goes away, no spectrum appears, and I get the following traceback:
>> 
>>>>> Exception in Tkinter callback
>> Traceback (most recent call last):
>>   File "/sw/lib/python2.4/lib-tk/Tkinter.py", line 1345, in __call__
>>     return self.func(*args)
>>   File
>> "/usr/local/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/OpenSpectrumPopup.py",
>> line 227, in openSpectra
>>     self.parent.finishInitSpectrum(spectrum)
>>   File "/usr/local/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/Analysis.py",
>> line 1351, in finishInitSpectrum
>>     self.initBlockFile(spectrum)
>>   File "/usr/local/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/Analysis.py",
>> line 1188, in initBlockFile
>>     Util.defaultContourLevels(spectrum)
>>   File "/usr/local/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/Util.py", line
>> 1273, in defaultContourLevels
>>     v = 3 * getNoiseEstimate(spectrum) /
>> spectrum.root.currentAnalysisProject.globalContourScale
>>   File
>> "/usr/local/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/ExperimentBasic.py",
>> line 517, in getNoiseEstimate
>>     d = block_file.getValue(pt)
>> BlockFile.error: could not get point: 201 390 493
>> 
>> Any ideas? The point numbers in the final line change with different
>> attempts but the rest of the error is consistent. Final note is that this
>> will be experiment #24 in the project.
>> 
>> Thanks,
>> Andrew


-- 
Dr. Andrew Fowler                 | University of Iowa
Associate Director                | B291 Carver Biomedical Research Building
Medical NMR Facility              | Iowa City, IA 52242
319-384-2937 (office)             | 319-335-7273 (fax)
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