Yes, non-blocked data = disaster. With pipe2azara you can specify the
block size (so the product of the number of points in each dimension of
the block). The default is 4096. That's probably ok for 3D data. For 4D
I'd probably use 16384 or something.
But even blocked data is going to be problematic if the data sets are
huge. Pre-calculated contour files might help (but obviously only after
peak picking). We're also thinking about other ways we might get around
this issue (but haven't come to any conclusions yet).
Wayne
On Fri, 11 Dec 2009, Andrew Fowler wrote:
> Hi Dominique,
>
> I'm not completely thrilled to learn this is still a problem, but I can
> provide the explanation that Wayne gave me and a relatively simple
> workaround.
>
> The "problem" is that NMRPipe uses a non-blocking data format. It's the way
> Frank chose to do things, and has never given me a problem in Pipe. In
> Analysis, the XY planes correspond to how Pipe stores data and don't cause
> problems. I THINK this requires the contouring routine in Analysis to deal
> with the entire dataset as one big chunk.
>
> The fairly easy workaround at the expense of some disk space is to convert
> the data into a blocking format. Analysis comes with pipe2azara which will
> do this, or you can use Sparky's pipe2ucsf. Assuming you're trying to get
> the spectrum set up in Analysis for the first time, this isn't a major
> problem.
>
> Cheers,
> Andrew
>
>
> On 12/11/09 2:46 PM, "Dominique Marion" <[log in to unmask]> wrote:
>
>> Using Analysis 2.1.2, I am still experiencing the same issue as described by
>> Andrew Fowler on May 15, 2008. When I try to contour nmrPipe files as XY
>> planes, this works fine. But when I switch to orthogonal planes, the virtual
>> memory of my iBook increases for ever. Wayne was claiming to have found the
>> error located in "slice_file.c". The issue seems to be still there... at
>> least on my settings.
>>
>> Dominique
>
> --
> 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)
> [log in to unmask]
>
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