Subject: Re: color code in sparky
From: Nicholas Fitzkee
Date: Dec 8, 2010

Previous: 770

Hi Amrita,

I saw your post in the NMRPipe discussion and was wondering exactly what you meant.  Franks response there was actually quite informative, and, like he said, there could be several reasons for seeing peaks of differing sign, or peaks with multiple-signed components.  From your description, it sounds like you have one of two problems: either youre selecting the wrong processing mode in the bruker/varian program (States vs. Echo-Antiecho), or you have a spectral artifact (e.g. phase twist).  One is simple to fix, the other corresponds to an problem with the pulse program.

The bottom line is that simply adjusting the color scheme probably isnt going to help you.  If youve processed the spectrum incorrectly, the peak positions are simply incorrect, and if there are artifacts, the observed ppms will be shifted from the real values. 

Im not expert at identifying artifacts, but my recommendation is this: submit a screenshot of your spectrum, noting where the problem is, to the NMRPipe list (or provide a web link in your email).  If youre using a standard bruker or varian pulse program, tell us what it is, or upload the pulse code if its something you came up with.  Finally, attach a copy of your processing scripts -- eg. fid.com and nmrproc.com .

You may not have any more luck with this approach, because people are very busy these days, but at least youll have provided the information needed to fix your problem.

Regards,
Nick Fitzkee