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]
|