Overlay spectra with different color

[jmgo...@ncsu.edu]

Hi Woonghee,

I was wondering if it was possible to change the color of the different spectra when overlaying them. Thanks in advance!

Best,

Jessica

[Lee, Woonghee]

Dear Jessica,

You can just type "ct" and change the color. Or, yoy can click tool button in the poky main window when selecting a spectrum and click contour setting button in the opened window if you use poky.

Best,

Woonghee

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From: nmr-s...@googlegroups.com <nmr-s...@googlegroups.com> on behalf of jmgo...@ncsu.edu <jmgo...@ncsu.edu>
Sent: Monday, July 5, 2021, 17:17
To: NMR POKY/SPARKY USER GROUP
Subject: [NMR POKY/SPARKY] Overlay spectra with different color

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[Gabriel Cornilescu]

May want to check out the select all/random colors from 'ec' - easy contour - a nice tool, I'm using it all the time with hsqc titrations. Even more useful, handling contour levels in multiple spectra is fast in 'ec'.

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/CY4PR05MB293412F7AFEA877BED323E0FEC1C9%40CY4PR05MB2934.namprd05.prod.outlook.com.

[Gabriel Cornilescu]

Jessica,

I've included below some other sparky commands/tricks that I'm using routinely with nmr titrations:

****** titr Sparky ********

yr - zoom in one spectrum will also zoom in all others (if syncronyzed with yt)

ct - 1-apo-blue, 2-magenta, 3- lime green, 4-orange, 5-red, then -> Set default
* ec - easy contour (use Update to see defaults from ct above)

* eo - easy overlay spectra

* pa, oc, op (to copy all apo peak labels onto next spectrum)
* pc - peak center (perturbed peaks), repeat onto the next spectrum etc. until the last spectrum - this way most shifting peaks will be assigned automatically in all spectra, manually inspect overlap regions and broadened out peaks

lt - check shifted amide peaks one by one (double click each assignment in sequence to jump into its zoomed spectral location in all spectra)

* np - perturbation plot
dHN = sqrt [dH^2+(dN/B)^2)/2], B=7, k=1/B=0.14
save to graphics/from_ndpplot.png

- edit YMAX=...ppm in ~/ndpplot.ini, if needed to normalize CSPs

* Click on 'Gradient' button, a new file called "p" will be written, with color gradient

* pt/Save (save as Z2445167076_zoom.ps)

*** Pymol:
pymol from_ndpplot.pse&

- color all blue to make sure previous color gradient is reset!!!

@p - on pymol command line to update colors from ndplot
File/Export as png: map_to_struct.png

[Lee, Woonghee]

Hi Gabriel,

 

This is really a nice note! Everybody will benefit from it.

 

Thanks,

Woonghee

 

--

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

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

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/163a6893-eee5-f6e1-d14d-752b179dbc45%40gmail.com.

[Jessica M. Gonzalez-Delgado]

Wow! Thank you so much for sharing these!!

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/B2A1B958-7146-4749-ADA6-55F6220D0AE2%40ucdenver.edu.

[Gabriel Cornilescu]

I also have an NMRPipe protocol to process all titration spectra (acquired with NUS) in a couple of seconds :)

Please let me know if you're interested...

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/8c87c851-bade-495e-bf64-bbdd34348f31%40ncsu.edu.

[stefano ciurli]

… who would not be…? :-)

Sent from my iPad

On Jul 6, 2021, at 19:10, Gabriel Cornilescu <gcorn...@gmail.com> wrote:



To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/74236ee1-1873-71e5-457d-07da48bcdcc3%40gmail.com.

[Gabriel Cornilescu]

I placed an example dataset here:

https://drive.google.com/file/d/1juQgtFH43SLxonV7Ke5jl3zK4C6miFdz/view?usp=sharing

Please take a look at the README file and feel free to ask questions.

Enjoy,

Gabriel