Fwd: Sparky NOE integration volume problem

[Woonghee Lee]

---------- Forwarded message ---------
From: Woonghee Lee <pines...@gmail.com>
Date: Tue, Sep 1, 2020 at 2:37 PM
Subject: Re: Sparky NOE integration volume problem
To: Indrani Pal <ip...@ksu.edu>

Dear Indrani,

Did you type "pi" for the selected peak to integrate? Do you see the circle instead of the box indicating that the peak has been integrated?

However, peak intensity and volume do not differ much in structure calculation. 

Best,

Woonghee

On Tue, Sep 1, 2020 at 2:11 PM Indrani Pal <ip...@ksu.edu> wrote:

Dear Dr. Woonghee Lee,

I am using sparky to integrate 3D 15N-1H NOE peaks. I am integrating all assigned peak through peak-->integrate-->gaussian fit method. But when  I am calling the peak list the volume column is not updating. It is staying blank. But I can see the peak height when I am updating it. 

I need the peak volumes to do a structure calculation. I want to know how can I fix this problem to get the peaklist populated with volume? 

Thank you very much in advance.

Regards,

Indrani

Research Associate

Department of Biochemistry and Molecular Biophysics

Kansas State University

Manhattan, KS - 66506

--

================================================

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

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.)

Denver, CO USA 80217-3364

woongh...@ucdenver.edu

https://sites.google.com/view/wlee-group 

 

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204 USA

--

================================================

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

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.)

Denver, CO USA 80217-3364

woongh...@ucdenver.edu

https://sites.google.com/view/wlee-group 

 

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204 USA

[Lee, Woonghee]

Dear Indrani,

 

“But there are many peaks which are not integrated due to 'bounding contour too large'. In that case”

 

That’s one of the reasons why using volume or fit height for structure calculation of a protein is sometimes unrealistic. You can play with fitting options in “it” window, but I don’t think it really matters.

 

If you have already assigned, there are two ways.

 

“gd” (continuous auto-NOE calibration) and “xf” (binning approach).

 

Also you can try “c3” plugin that will auto-run structure calculation along with NOE assignments.

 

Best,

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.)

Denver, CO USA 80217-3364

woongh...@ucdenver.edu

https://sites.google.com/view/wlee-group 

 

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204 USA

 

From: Indrani Pal <ip...@ksu.edu>
Date: Wednesday, September 2, 2020 at 7:35 AM
To: "Lee, Woonghee" <WOONGH...@UCDENVER.EDU>
Subject: Re: Sparky NOE integration volume problem

 

Dear Dr. Woonghee Lee,

 

Thank you very much for your immediate response and for helping me out with this problem.

 

Yesterday, I did pi for the selected peaks and I can see the circle instead of the box for the integrated peaks. Now it is populating. But there are many peaks which are not integrated due to 'bounding contour too large'. In that case, I am thinking to convert the peak heights to upper limit distance constraints. I would like to know is there a way to convert the peak heights to upl (xeasy format) in Sparky? 

 

I did xe to write the peak heights in xeasy format. But can I convert it to upl?

 

Thank you again.

 

Regards,

Indrani

 

 

 

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From: Woonghee Lee <pines...@gmail.com>
Sent: Tuesday, September 1, 2020 3:37 PM
To: Indrani Pal <ip...@ksu.edu>
Subject: Re: Sparky NOE integration volume problem

 

Dear Indrani,