Titration zoom-up plots

[Erik Walinda]

Dear Dr. Lee and fellow users,

I finished reading the bioinformatics article and now I wonder if the following would be possible using POKY automation scripting. I have experience with SPARKY but am not completely up-to-date on the new developments.

So right now, I have 6 titration spectra loaded in POKY, 0 to 6.ucsf in the overlaid view using the easy-overlay window. Thanks to the youtube videos and command index, I learned how to set contours and choose colors etc.

Now, for each of the ~80 HSQC peaks, I want to make a subplot that zooms onto the peak and prints the current zoom-up as a single PDF.

I do not mind manually setting the ROIs if necessary. Alternatively, they could be +/- X ppm around the peak center.

So the logic would be something like:

for peak in listOfPeaks:

  setROI()

  printCurrentWindow("peak~number.pdf")

If I knew the internal functions of POKY it seems quite straightforward. How do you think?

[Needless to say, this could be done manually. The problem would be that for each small color or contour level change, I need to go back and re-do all 80 peaks (and I have more data and plan more titrations in the future ...)].

I saw this on github and perhaps this might be a starting point. But perhaps somebody already has something closer?

POKY/Poky_Batch_Scripts/plot_batch.py at master · pokynmr/POKY (github.com) 

Best wishes,

Erik Walinda (Kyoto University)

[Lee, Woonghee]

Dear Dr. Walinda,

 

In the POKY Notepad, go Poky Script -> Find Additional….

 

Then select save_peak_plot_script.py. It will do what you want. Select a few peaks, zoom in for the wanted extent, then run by cmd/ctrl+b or from File -> Run Python Module.

 

Best,

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A (office), Rm 4128 (dry lab), Rm 4133 (wet lab)

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

 

From: nmr-s...@googlegroups.com <nmr-s...@googlegroups.com> on behalf of Erik Walinda <arumo...@gmail.com>
Date: Sunday, August 25, 2024 at 2:56 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] Titration zoom-up plots

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