Subject: Re: R: [nmr_sparky] noe distance restraints
From: Marco Sette
Date: Sep 28, 2012

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Hi Werkawi

for question 1 I suggest you to llok at the NOESY, judge yourself which can be medium or strong, may be using some NOES on fixed distances and then make a classification. Its quite empirical, I agree. May be someone has better hints.
For question 2 a python script should suffice. Im not expert in python, Im studying now, but will try to prepare something in the week-end, its a nice exercise ;-)

ciao ciao
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

--- Ven 28/9/12, Ariam Isak ariamisak@... ha scritto:

Da: Ariam Isak ariamisak@...
Oggetto: Re: R: [nmr_sparky] noe distance restraints
A: nmr_sparky@yahoogroups.com nmr_sparky@yahoogroups.com
Data: Venerdì 28 settembre 2012, 20:53

Cio Marco,

Thanks for the timely reply.
I have already saved the file as a list file andi know i have to classify the peaks based on thier intesnisty into weak and strong.the problem is;
1. how do i determine the cut-off intensity for the weak or strong or medium while grouping.
2. what programs to use to group the thousands of noe peaks i have.
Detail info would be great, i am a newbie in this area.

Grazie Mille
Werkawi
From: Marco Sette m77it@...
To: nmr_sparky@yahoogroups.com
Sent: Thursday, September 27, 2012 12:56 PM
Subject: R: [nmr_sparky] noe distance restraints


Hi Werkawi,

the peak list you generate with lt after integration can be saved in a .list file.
This file can be the input for some program, in python or the language you prefere, to group the peaks as weak (below an assigned value), medium or strong.
Ciao ciao
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

--- Gio 27/9/12, werkawi ariamisak@... ha scritto:

Da: werkawi ariamisak@...
Oggetto: [nmr_sparky] noe distance restraints
A: nmr_sparky@yahoogroups.com
Data: Giovedì 27 settembre 2012, 21:41

Hello Sparky users,

i want to generate distance retraints from the Noe peak volumes i have. sofar i have integrated all the peaks and i tried to classify them into bins (strong , medium, weak noes) but it didnt work.can any one give me more detailed information on how to do this. thanks.

Werkawi