Tuesday, November 07, 2006

Pipe mentality

An helpful wiki/tutorial of NMRPipe serves as a review as well. A few excerpts will give you a picture of the proteinist mentality (to be compared with the CW mentality).
It is important to realize that processing this data requires you to frequently exit and enter NMRPipe to work with text editors and invoke commands on command lines.
then left-click on “Execute” to apply a cosine-bell (90°-shifted sine-bell) window function. [...] Write down the parameters used for this function because you’ll need to enter them into your script later.
Once you are satisfied with the phasing of your spectrum, write down the P0 and P1 values so you can use them in your processing script.
The script shown above should produce a good spectrum under most circumstances.
Edit parameters for processing the indirect dimension. You don’t get to see a 1D spectrum to help you alter these parameters. In the NMRPipe procedure, you just process the 2D spectrum as a whole, read it into the GUI, make observations and phase adjustments in the GUI, then return to this script, alter it, and reprocess the spectrum.

Processing a 2D spectrum with NMRPipe is a ritual. If you are going to spend 2 weeks (or more) to assign your spectrum, why not spending a whole morning to process it? In iNMR you get the same results with:

  • two clicks on the "gears" icon;
  • one click on the manual phase correction icon, followed by the interactive adjustment of the whole matrix;
  • one click on the automatic baseline correction icon.

From the tutorial I get the impression that the majority of NMRPipe users spend their time in copying the same script with the same default commands in all their folders, to get the same standard processing (see text in bold). What's the point? How did they arrive there? NMRPipe started as a program for programmers. Modifying the script the user can save the half-processed spectrum at any time, apply on it another program (likely written by himself), then return to NMRPipe. In a different scenario, the user can just learn to write the scripts (a basic form of programming) and experiment with custom work-flows. NMRPipe is a useful tool and it's simple to understand. Being it free, it's also popular. When it appeared, it obviously looked more advanced than now.
The "proteinist mentality" thinks: 1D NMR belongs to the past; NMR and "Protein NMR" are the same thing; I'll write my own plug-ins for whichever program I am gonna use.
I am exaggerating! I can't say I know a single person who thinks in this way. Still I have often heard the observation that there is ample choice of software, both commercial and free, and no space for a new product. When you carefully compare two programs, you can actually notice so vast differences in approach to justify their simultaneous existence.
I don't know if the popularity of NMRPipe is still growing or decreasing. For years, I have been visiting weekly a "Large Research Infrastructure"where 90% or more of the researches preferred XWin-NMR and TopSpin, and my impression is that the latter peaked at the 100%. Is NMR processing so mature that the industrial product has superseded the research tool? Or is Bruker investing, at last, big money in software? Or, more simply, people had enough of command line tools?


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