Ankur,
If you picked your peaks (semi)automatically - i.e. with Shift+Ctrl+mouse drag, then they are already integrated. Ones that you placed by hand (Ctrl+click) may not be - if you have any like this you should re-fit them (e.g. using the Recalc Fit button in the Edit Peaks popup).
height = intensity = value of highest point near the peak position (which may not be on a data point)
volume = integral = by default this is the sum of the value of the data points with in the box around the peak (box sum)
You can change the fit to one of 3 functions and refit - linewidths will then appear in the columns in the data table - if that is what you require. I think mostly people use the box sum data, but it would depend on your application.
Hope that helps
Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
College of Medical, Veterinary & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089
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The University of Glasgow, charity number SC004401
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From: CcpNmr software mailing list [[log in to unmask]] on behalf of Ankur Jalan [[log in to unmask]]
Sent: 28 October 2016 11:17
To: [log in to unmask]
Subject: NOE Peak Integration in ccpnmr 2.4
Hello Everyone,
First of all, I'm very grateful to the developers of this amazing program. I like the ccpnmr program. I have used it to assign the peaks (TOCSY and ROESY/NOESY) on my 12 amino acid long peptides.
I understand that there must be several discussions here which talk about the NOE peak integration. I tried to look for them, but I was lost while going through them. I'm sorry as I.m not very good at it.
I have assigned my peaks and now I want to integrate them to see how close the residues are. I am a novice at it, and the professors I work with have never used the ccpn to integrate NOESY peaks (proton-proton). I hope you guys can help me to get started with the NOE peak integration. I will be very grateful to all of you if you can help me with it. My adviser suggested me to use SPARKY. But, I think ccpnmr is a very good program and I can learn how to use it wisely rather than switching to a totally different program.
Please suggest me to how to get started with the NOE peak integration. I have tried to go to peak---> peak table. I see the assignments I made and it gives me height and volume of those peaks. I don't understand what these values are. I also columns which says merit (it is filled with 1.0) , fit method (parabolic) and vol. method. I want to figure out how strong or weak some NOE peaks are. I have heard that the peak volume can tell me how intense these peaks are. But, I can't comprehend the these volume numbers. What do they signify?
Please help me out. I will be very grateful to all of you for any help.
Best Regards,
Ankur Jalan
Ph.D. Candidate
Brigham Young University, Provo,USA.
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