Subject: Re: [nmr_sparky] Re: Using Sparky with Python
From: Josh Ward
Date: Oct 19, 2005

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So, what kind of data are you looking at exactly? I am assuming you are
working on backbone/NOESY assignments from the sounds of things. Oh,
and rereading your inital e-mail, I gather that the bad data has been
shipped to you from your collaborator? Is that right? If so....I am
sooo sorry! Hang in there, youll figure it out. :) I wish I knew
anything at all about the Felix matrix format. If it is just a label
issue, you could probably proceed as is since ther error should just be
cosmetic. But that is all going to depend on the experiment you are
looking at I suppose.

A decent book for the data processing theory that I have found is, NMR
Data Processing by Jeffrey Hoch and Alan Stern (1996) You can find it
on Amazon ISBN: 0471039004 That should hopefully help you figure out
data handling between the spectrometer and sparky. As far as how to
handle the basics of assignment...I wish I had found a good book and /
or review for that!

Here are some cool resources I have uncovered with google regarding
assignment, though:
http://www.embl-heidelberg.de/nmr/sattler/teaching/
http://structbio.vanderbilt.edu/~chazin/Biochem_301.Lecture-notes/N.M.R/Bioch-301.2.ppt

Also check out MARS, a brilliant autoassignment program that is easily
used in conjunction with sparky once you have data.

http://www.spincore.com/nmrinfo/MARS.html
http://www.mpibpc.gwdg.de/abteilungen/030/zweckstetter/

Ras Al Jdi Mai wrote:

Thanks, Josh!

I emailed the guy about nmr pipe. Id actually heard of it already just
from reading about about all this stuff. Youre not kidding about the
steep learning curve! Man, oh man!

I get, in theory, what the machine does since I take alot of physics
classes, but Im feeling kind of lost when it comes to interacting with
the data. Since the data is messed up, we cant do any peak picking yet
and I feel REALLY lost in that area. Do they have an NMR Assignment
how to, for Dummies???? I mean, I can work sparky, the manuals
actually not too bad as manuals go, and I understand the theory about
whats going on, the interactions the machine is taking data on, but
how do I connect those two areas into an Oh, I need to do this kinda
thing? Can you recommend any books?

Thanks, again!
-R







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--
Josh Ward
Graduate Research Assistant
Purdue University
Department of Medicinal Chemistry and Molecular Pharamacology
Lily Hall of Life Sciences
Phone: (765) 494-2191