Perturbation Plot Not Analyzing
Bryce Ackermann
[Mac, Most recent version, perturbation plot, NH HSQC]
Lee, Woonghee
Hi,
- Does the assignment format follow this rule? Like G1 in the Group, H in the Atom.
- The number of peaks and assignments must be the same between two spectra.
Keep “py” window opened while you are doing it. It will inform you some clues about.
Woonghee Lee, I.E.I.P., M.S., Ph.D.
Assistant Professor & Data Science and Chemistry Certificate Program Director
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
https://poky.clas.ucdenver.edu
https://poky.clas.ucdenver.edu/wlee-group
https://clas.ucdenver.edu/chemistry/woonghee-lee
https://clas.ucdenver.edu/chemistry/data-science-and-chemistry-certificate
Shipping/Mailing Address:
Woonghee Lee
1201 5th 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 Bryce Ackermann <backer...@gmail.com>
Date: Thursday, April 24, 2025 at 2:23 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] Perturbation Plot Not Analyzing
|
You don't often get email from backer...@gmail.com. Learn why this is important |
|
[External Email - Use Caution] |
--
You received this message because you are subscribed to the Google Groups "NMR POKY/SPARKY USER GROUP" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
nmr-sparky+...@googlegroups.com.
To view this discussion visit
https://groups.google.com/d/msgid/nmr-sparky/44a03fa4-6f02-4394-9dc0-db7dd97fb3c8n%40googlegroups.com.
Bryce Ackermann
On Apr 24, 2025, at 1:39 PM, Lee, Woonghee <WOONGH...@UCDENVER.EDU> wrote:
Hi,
- Does the assignment format follow this rule? Like G1 in the Group, H in the Atom.
- The number of peaks and assignments must be the same between two spectra.
Keep “py” window opened while you are doing it. It will inform you some clues about.
Woonghee Lee, I.E.I.P., M.S., Ph.D.Assistant Professor & Data Science and Chemistry Certificate Program DirectorDepartment of ChemistryUniversity of Colorado Denver1151 Arapahoe St. (Science Bldg.) Rm 4128A (office), Rm 4128 (dry lab), Rm 4133 (wet lab)Denver, CO 80217-3364, USAOffice: +1-303-315-7672
Shipping/Mailing Address:Woonghee Lee1201 5th St. UCD CHEM-194P.O. Box 173364 (USPS)Denver, CO 80204, USA
stefano ciurli
Dear Woonghee,
I am trying to fit relaxation data using the ‘rh’ protocol in POKY.
It worked well for a set of experiments, but it did not for another set, and I do not understand why. I am sure the tau values and the spectra correspond well, but I see the following:
Additionally, using the following setup…
I notice that the headings of the columns are strange (see 1.25e+03/3)
Finally, it seems that I cannot use replicate experiments with the same tau value, it excludes them by defaulr.
Woonghee, if necessary, I can send you the data separately.
Stefano
Lee, Woonghee
Sent: Friday, April 25, 2025 5:26:49 AM
To: Lee, Woonghee <WOONGH...@UCDENVER.EDU>
Cc: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Perturbation Plot Not Analyzing
|
[External Email - Use Caution]
|
Dear Woonghee,
Lee, Woonghee
Hi Stefano,
1.25e+03/3 misses the last 0 due to the available column size.
It seems “rh” did right. One potential problem is due to Bruker’s “NC_PROC”.
21: 9
22: 7 – need to be divided by 4
23: 9
24: 7 – need to be divided by 4
25: 9
26: 9
27: 9
28: 8 – need to be divided by 2
29: 9
30: 7 – need to be divided by 4
Simply, you can open POKY Notepad -> File -> Script -> Find Additional…
Then apply 0.5 to 28 and 0.25 to 22, 24, 30. That will fix the issue.
Best,
Woonghee Lee, I.E.I.P., M.S., Ph.D.
Assistant Professor & Data Science and Chemistry Certificate Program Director
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
Shipping/Mailing Address:
Woonghee Lee
1201 5th St. UCD CHEM-194
P.O. Box 173364 (USPS)
Denver, CO 80204, USA
Date: Friday, April 25, 2025 at 5:26 AM
To: Lee, Woonghee <WOONGH...@UCDENVER.EDU>
Cc: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Perturbation Plot Not Analyzing
|
[External Email - Use Caution] |
Dear Woonghee,
stefano ciurli
Hi Woonghee,
It worked, thanks!
However, it would be better not to have to do this trick. Is it possible to tweak the software to avoid this?
Moreover, is it possible to have the software accept replicates?
Stefano
Lee, Woonghee
Hi Stefano,
Good to know it worked. Workaround for using replicates can be using time parameters with neglectable decimals like 10.00001. For ncproc, I think you have used nmrpipe for the processing, then converted ucsf from ft2. Since nmrpipe didn’t adjust intensities based on ncproc, poky has had no clue about this scaling. If you converted from 2rr, POKY would have compensated the ncproc parameter. Hope this helps.
Woonghee Lee, I.E.I.P., M.S., Ph.D.
Assistant Professor & Data Science and Chemistry Certificate Program Director
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
https://poky.clas.ucdenver.edu
https://poky.clas.ucdenver.edu/wlee-group
https://clas.ucdenver.edu/chemistry/woonghee-lee
https://clas.ucdenver.edu/chemistry/data-science-and-chemistry-certificate
Shipping/Mailing Address:
Woonghee Lee
1201 5th St. UCD CHEM-194
P.O. Box 173364 (USPS)
Denver, CO 80204, USA
stefano ciurli
Hello,
Is there a way to plot different spectra (N-HSQC) with intensities normalized with respect to a reference spectrum?
Stefano
Lee, Woonghee
Hi Stefano,
Just uploaded the new script “normalize_spectrum_script.py” that you can use from Poky Notepad “Pn”.
File -> Poky Scripts -> Find Additional …
It will be there. Ctrl or CMD + b to run.
Best,
Woonghee Lee, I.E.I.P., M.S., Ph.D.
Assistant Professor & Data Science and Chemistry Certificate Program Director
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
https://poky.clas.ucdenver.edu
https://poky.clas.ucdenver.edu/wlee-group
https://clas.ucdenver.edu/chemistry/woonghee-lee
https://clas.ucdenver.edu/chemistry/data-science-and-chemistry-certificate
Shipping/Mailing Address:
Woonghee Lee
1201 5th St. UCD CHEM-194
P.O. Box 173364 (USPS)
Denver, CO 80204, USA
From:
stefano ciurli <stefano...@gmail.com>
Date: Thursday, May 15, 2025 at 11:00 PM
To: Lee, Woonghee <WOONGH...@UCDENVER.EDU>
Cc: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Normalised contours
|
[External Email - Use Caution] |
Hello,
stefano ciurli
Hi Woonghee,
Thank you for the speedy response. This script produces a new spectrum.ucsf that one needs to load back into the project, and that is fine.
My idea was to simply plot the existing spectra in a project (relaxation study) without having to produce a new spectrum.ucsf. Moreover, the script allows me to normalize one spectrum wrt a reference spectrum, and not a series of spectra at once.
Stefano
Lee, Woonghee
Hi Stefano,
Generating normalized spectra would indeed be more convenient if you want to plot specific regions as you like when combined with synchronization ("yt"), uniform contour levels ("uc"), and uniform view size ("us"). I was thinking of simply plotting a bunch of selected spectra, but where to plot would be unclear unless you only plot the full extent. So, I’ve uploaded the updated version (with the same script name) that supports multiple spectra at once.
stefano ciurli
Thank you, Woonghee!