Subject: R: [nmr_sparky] Re: distance constraints from NOESY crosspeaks
From: Marco Sette
Date: Feb 12, 2012

Previous: 815


A single spectrum at 300 ms contains a lot of spin diffusion. Its good to assign DNA/RNA not for constraints.
Try to use something like 50 ms instead.

Marco



Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology
University of Rome, Tor Vergata
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail: sette@...
e-mail: m77it@...
Tel.: +39-0672594424
Fax: +39-0672594328

www.rete29aprile.it

--- Dom 12/2/12, jennig148 claudia.gerlach@... ha scritto:

Da: jennig148 claudia.gerlach@...
Oggetto: [nmr_sparky] Re: distance constraints from NOESY crosspeaks
A: nmr_sparky@yahoogroups.com
Data: Domenica 12 febbraio 2012, 16:23

No, i have only a spectrum with a mixing time of 300ms.

--- In nmr_sparky@yahoogroups.com , Zhi Liu liufanghe@... wrote:

Did you do the build up with different mixing time?Jay

From: jennig148 claudia.gerlach@...

To: nmr_sparky@yahoogroups.com
Sent: Friday, February 10, 2012 7:24 AM
Subject: [nmr_sparky] distance constraints from NOESY crosspeaks


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Hello users,

I have a NOESY spectrum of a DNA/RNA strand. I try to get the distance constraints by integration of the NOESY crosspeaks and then converting the volumes into distances.

For calibration i want to use the C H5-H6 crosspeak intensity (2.5 A).
I found the following equation in one message:

distance = 2.5 * (intensity of peak/intensity of C H5-H6 peak) ^ (1/6)

But most of the distances are coming out are too short.

Another equation i found was:

distance =(intensity of peak^(-1/6)-A)*C

But here i dont know what A and C is.

So the question is: What is the correct equation to calculate the distances?

Thanks