Hello,
I wanted to post a follow up on this old message from last year,
regarding pseudo-3D data. I used the pipe2azara script to generate a
pseudo-3D azara file and read that into an existing analysis project.
That seemed to work fine and it recognized that it was a pseudo-3D and
even read out the parameter values that I had specified in the different
2D slices of the nmrpipe files (using the sethdr program). However,
there were a couple of odd things I wanted to report.
I was unable to assign any peaks in the third (and final) slice/plane of
the pseudo-3D. I was able to pick peaks in all three planes and was able
to use the 'a' shortcut to assign the first two planes, but there was no
response to me hitting 'a' in the third plane. Note that there were no
error messages on the command line. Note that I was also unable to just
select those picked peaks by just clicking on them (dragging around them
does work tho).
The other thing I noticed is that it did not show up as an experiment
series in the rates analysis window. I had to manually click the 'edit
series' button, where I found out that not all information had been
entered for the experiment to be recognized as a proper series.
Specifically the condition type and units for the values. Perhaps it
would make sense to pop up that dialog box when a pseudo-3D is loaded
into the program?
Otherwise things seem to work well and I managed to do some test rate
analysis on the data. By applying the group assign option I did manage
to get the third plane assigned, in a roundabout way.
Patrick
Wayne Boucher wrote:
> Hello,
>
> Thanks to data and tips provided by Patrick van der Wel, I've now
> (hopefully correctly) added in support for pseudo 3D data (and in theory
> pseudo ND data) in NMRPipe. (Such support already existed for Azara
> format.) It seems that NMRPipe specifies the nucleus type to be ID for
> these pseudo dimensions. So now the program will detect this.
>
> The Analysis program still only reads the full NMRPipe single-file format,
> not the multi-file format. But to get at the values automatically you
> need to access the multi files (since only one value, for the first plane,
> is stored in the single file). So when you select the single file in
> OpenSpectrumPopup it will bring up a dialog asking if it really is pseudo
> 3D (and if not it will remove the offending dimension) and what the values
> of the planes are. You can either type in the values by hand, in which
> case you don't need access to the multi files at all, or let the values be
> fetched from the multi files after you specify the directory and template
> (with the %03d) for the files.
>
> (You will see that the "template" label in that dialog is a button. If
> you hit that button it will let you select a file in the relevant
> directory. Just select any of the multi files and hit ok. Then edit the
> name to replace the 001, or whatever, with %03d. This could try an be a
> bit cleverer and do that replacement automatically but I haven't put that
> in yet.)
>
> I have also updated the pipe2azara script, which is capable of dealing
> with the multi-file format, so that it automatically determines the values
> if you give it the multi-file template. This script will actually block
> the data, so has some advantage over importing the single-file NMRPipe
> data into Analysis. So, first convert the data to Azara format and then
> import into Analysis. (Well, for smallish data files this is no great
> advantage.) (I also fixed an unrelated bug in pipe2azara.)
>
> At some point we ought to add in a way of specifying that the other file
> formats, besides Azara and NMRPipe, are pseudo ND and bring up a similar
> dialog, except that the values would have to be definitely entered by
> hand.
>
> Wayne
>
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