I'm not sure about the legalities of including the pipe2xyz code (is this
NIH copyright?), but I'll look into that as well.
Regards, Wayne
On Tue, 12 Apr 2005, Andrew Herbert wrote:
> What I had in mind was a simple system call & if possible including the
> pipe2xyz code with analysis. I thought this could be a quick & dirty
> way of having rudimentry support for the NMRpipe format
>
> Andy
>
>
> On Tue, 2005-04-12 at 15:52, Wayne Boucher wrote:
> > Do you mean as a system call? That should be easy enough (certainly if
> > pipe2xyz runs just by giving it a bunch of commands). I'll look into
> > that.
> >
> > Wayne
> >
> > On Tue, 12 Apr 2005, Andrew Herbert wrote:
> >
> > > Would it be possible to incorporate running the pipe2xyz script from
> > > within analysis?
> > >
> > >
> > > On Tue, 2005-04-12 at 14:42, Wayne Boucher wrote:
> > > > Right, hopefully someone else can do a better job of answering this than
> > > > me. I have never used NMRPipe so am rather ignorant about it all. But
> > > > the way I understand it, the native format for NMRPipe is plane oriented,
> > > > and you end up with one file for each plane. Analysis definitely
> > > > (currently) does not understand the plane files (Analysis assumes one file
> > > > per spectrum). There is this program pipe2xyz which converts the plane
> > > > files into one file, and the output of that is what Analysis understands
> > > > by "NMRPipe" format. So if you have an example where importing that fails
> > > > then it would be useful if (somehow) we could get hold of the example (or
> > > > a smallest example where Analysis fails), so we could examine the header
> > > > here. (Well, if you know how to strip out the first 2048 bytes, e.g.
> > > > using dd, then that is the header so just emailing that should do the
> > > > trick, as well as telling us the total number of bytes in the file so we
> > > > can use that as a check.)
> > > >
> > > > It's possible someone in the dim and distant past has written a script to
> > > > convert from the NMRPipe plane files to Ansig/Azara format, rather than
> > > > going via the pipe2xyz script, and if so that would be an alternative.
> > > > As it is you will definitely need to run at least one script to get away
> > > > from the plane files, and we definitely want to support the output of
> > > > pipe2xyz, so that would be the recommended way.
> > > >
> > > > Regards, Wayne
> > > >
> > > > On Tue, 12 Apr 2005, Aura wrote:
> > > >
> > > > > hi everybody,
> > > > >
> > > > > Here is a new person which joined very recently the NMR protein field...
> > > > > Now, I'm trying to open with CCPNMR Analysis1.0.1 some 3D spectra already
> > > > > proccesed with NMRPipe, but I don't know how. I select the "file format" to
> > > > > NMRPipe in the OpenSpectrum PopUp Window, but I can only read in the
> > > > > individual planes (.ft3 files) not the complete transformed spectra.
> > > > >
> > > > > I can convert my spectra to nmrview matrix files but I cannot open these in
> > > > > Analysis. What is the easiest way to be able to view my 3D spectra in
> > > > > Analysis? Should I convert my files to the ANSIG format? If so is there a
> > > > > command in nmrpipe to output to ANSIG instead on nmrview?
> > > > >
> > > > >
> > > > > Thank you for your help,
> > > > > Aura
> > > > >
> > > --
> > > Dr Andy Herbert
> > > Department of Chemistry
> > > University of Edinburgh
> > > West Mains Road
> > > Edinburgh
> > > UK
> > > EH9 3JJ
> > > Tel: +44 (0)131 650 4704 or 650 7372
> > > Email: [log in to unmask]
> > >
> --
> Dr Andy Herbert
> Department of Chemistry
> University of Edinburgh
> West Mains Road
> Edinburgh
> UK
> EH9 3JJ
> Tel: +44 (0)131 650 4704 or 650 7372
> Email: [log in to unmask]
>
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