I have been attempting to automate processing in NMRPipe and have been running into small problems when processing my data vs processing the tutorial data.
Firstly, does an "autophase" or "interactive phase" option exist for NMRPipe? I have been able to get my data to phase, but doing it step by step in the macro editor is a bit cumbersome. This would be a great convenience.
Secondly, I have tried to peak pick my data, and I get an error that in the terminal window looks like
"sh: 1: .pk/tcl: Permission Denied"
and the peak detect does nothing. Is there a permissions problem in the file that I constructed to peak pick from?
As far as I'm aware there is only "auto-phase" for 1D experiments. For 2D data you can view the spectrum in nmrDraw and interactively phase the spectrum, extract the phase values and reprocess. I know Frank (the author of the software) has been working quite a lot on various extensions so to would be worth posting this message on the NMRPipe mailing list in case there is a new feature I'm unaware of.
I can't help you with the error, I've not seen it before. I assume you have set your environment variables and are using tcsh? Beyond that, again ask Frank via the mailing list, it is very active and friendly/helpful group.
Process and phase in Topspin, then use the AU program convert2pipe.ecj36 (attached). Phase correction values and transferred into the conversion and processing scripts. Use these scripts for processing in pipe.
Thanks again Clemens, I have had time to run with this, and it works great!
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