New Version?

[Nicholas Fitzkee]

Hi all,

Sometime between this morning and now the version was updated from h to i. I literally just finished installing version h; is there a good motivation for doing it again?

Thanks!

Nick

[Lee, Woonghee]

Hi Nick,

 

The new version has the BLASTP against BMRB (“bb”) and Run N-HSQC peak matching “RP”.

 

“bb” query and N-HSQC simulation overlaid on the experimental N-HSQC down here.

 

 

 

 

“RP” does weighted bipartite graph based peak matching between two N-HSQC.

 

For example, you simulate N-HSQC with “CS”, you get simulated N-HSQC with assigned peaks.

 

 

Left is experimental data with unassigned peaks, and right is from “CS” simulation (“E1” can be used for SHIFTX2 version).

 

 

 

Then, “RP”.

 

 

Floating labels are not to be certain. PINE Assigner “pr” can be used to evaluate further with probability/score.

 

 

My group were about to make a tutorial video on this, but you were faster!

 

Cheers,

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

woongh...@ucdenver.edu

 

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 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 Nicholas Fitzkee <nickf...@gmail.com>
Date: Tuesday, April 29, 2025 at 3:38 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] New Version?

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[Nicholas Fitzkee]

Awesome, thanks for the update! Definitely looks like it will be worthwhile to copy the new version. Especially since the process is still fresh in my mind!

Thanks again,

Nick

--

Nicholas Fitzkee

nickf...@gmail.com

Fitzkee Lab Research: We study how proteins interact with nanoparticles. When proteins bind, they form a corona on the nanoparticle surface. The diversity of proteins in fluids like blood makes it hard to predict which ones dominate. This matters: protein behavior in the corona shapes the immune response. Not all nanoparticles behave the same way. By understanding the corona, we aim to control how the body reacts.

We also study bacterial infections on surfaces, called biofilms. Biofilms on hip and knee implants are tough to treat. We’re working toward non-surgical solutions.

U.S. taxpayers fund our work through grants from the National Science Foundation and the National Institutes of Health. We are grateful for this support. Over 14 years, these grants have supported 30 jobs in Starkville, from undergraduates to research scientists. At MSU, our lab has produced nine Ph.D. and five M.S. degrees.

[stefano ciurli]

Dear all,

Am I the only one experiencing a terribly slow Enable/Disable action in POKY Analyzer? Is it always this slow?

Also, it does not appear to allow me to select multiple constraints by click-and-drag: is it OK?

Stefano

[Lee, Woonghee]

Hi Stefano,

Multiple restraints at once are not supported supposedly to push careful validation. 

Older macs are the slowest. But it isn't that bad if you go one restraint by one. It can be different reasons. Slow hdd, running out of ram, etc. Maybe you can open a terminal and see "top" and "free". Have you tried other computers/OSs?

Best,

Woonghee Lee, Ph.D.

Assistant Professor of Chemistry & Data Science and Chemistry Certificate Program Director

University of Colorado Denver

woongh...@ucdenver.edu

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

Sent from iPhone

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From: stefano ciurli <stefano...@gmail.com>
Sent: Wednesday, April 30, 2025 4:55:05 AM
To: Lee, Woonghee <WOONGH...@ucdenver.edu>; NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Slow Analyzer

 

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Dear all,

[stefano ciurli]

Hi Woonghee,

My wrong impression derives from looking at the YT tutorial. One by one is fine with me, thanks!
Stefano