Comments below
-------------------------------------------
Dr Gary S Thompson
NMR Facility Manager
Wellcome Trust Biomolecular NMR Facility
School of Biosciences, University of Kent,
Canterbury, Kent, England, CT2 7NZ
tel: 01227 82 7117<tel:01227%2082%207117>
e-mail: [log in to unmask]<mailto:[log in to unmask]>
orchid: orcid.org/0000-0001-9399-7636<http://orcid.org/0000-0001-9399-7636>
-------------------------------------------
On 23 Jan 2019, at 16:15, Brian Smith <[log in to unmask]<mailto:[log in to unmask]>> wrote:
I think automated matching will still fail when the spread of potential matches for hump of a peak is wider than the assignment tolerance.
This would indicate that either the shift list and now data don’t agree or that the assignment tolerance is too narrow. There an article that discusses tolerances and urges against using tolerances that are too tight
Journal of Biomolecular NMR<https://link.springer.com/journal/10858>
January 2005, Volume 31, Issue 1<https://link.springer.com/journal/10858/31/1/page/1>, pp 21–34| Cite as<https://link.springer.com/article/10.1007%2Fs10858-004-5359-4#citeas>
Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data
* Authors<https://link.springer.com/article/10.1007%2Fs10858-004-5359-4#authors>
* Authors and affiliations<https://link.springer.com/article/10.1007%2Fs10858-004-5359-4#authorsandaffiliations>
* Michele Fossi
* Jens Linge
* Dirk Labudde
* Dietmar Leitner
* Michael Nilges
* Hartmut Oschkinat
You're right that manually assigned peaks should be handled correctly - so pick a single peak and then make all the possible assignments for the whole hump manually. Thus the combined height/volume will be distributed between all the possibilities correctly, and depending how hard you push your disambiguation criteria there should be no problem (i.e. don't use the default ARIA settings where the "Ambiguity cutoff" drops rather low in later iterations). To stop these assignments polluting your chemical shift list, downweight the NOESY peak list (Experiments->Spectra->Tolerances->Shift Weighting).
Regards
Gary
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
----------------------------------------------------------------------
The University of Glasgow, charity number SC004401
________________________________
From: CcpNmr software mailing list [[log in to unmask]<mailto:[log in to unmask]>] on behalf of Gary Thompson [[log in to unmask]<mailto:[log in to unmask]>]
Sent: 23 January 2019 14:46
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: merged peak height
Hi
The aria automated and manual assignment protocols should be able cope with this as it treats peaks as multi component? I am sure I have used multi component peaks in both a manual and in an automated fashion (though you may need some extra macros to make the manual version work)
regards
Gary
On 23 Jan 2019, at 13:42, Brian Smith <[log in to unmask]<mailto:[log in to unmask]>> wrote:
I would suggest that if multiple crosspeaks are overlapped such that they merge into a long hump that’s wider than your tolerance for generating ambiguous restraints, then you should not be using them to generate distance restraints using most current structure calculation software since they do not usually handle generating an appropriately ambiguous restraint to include all the possibilities. You can leave the peak present, but use the “set merit” functionality to make it easy to exclude from subsequent restraint generation.
What is really wanted is that peaks should each have a “footprint” within which chemical shift matches can be made when generating ambiguous restraints.
From: CcpNmr software mailing list <[log in to unmask]<mailto:[log in to unmask]>> On Behalf Of Xiaowei Chen
Sent: 23 January 2019 13:13
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: merged peak height
Dear all,
I am correcting the wrong NOE in NOESY-HSQC now.
i met some problems: 2 peaks which are close to each other, they merged into one long peak. So i add 2 peaks at one place. When ccpnmr calculate the height of each peak, it set them as same number . if i delete one peak, the height of the other peak does not change.
it seems the ccpnmr can not seperate 2 peaks at that point. In my later work, the 2 distance are both very short.
I noticed that there is a "peak seperator" which can seperate 2 merged peaks automatically. But i can not find it in CCPNMR 2.4
So, do you know where is the peak seperator or is there other method to seperate them?
Thank you in advance.
Xiaowei
________________________________
To unsubscribe from the CCPNMR list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPNMR&A=1
________________________________
To unsubscribe from the CCPNMR list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPNMR&A=1
________________________________
To unsubscribe from the CCPNMR list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPNMR&A=1
________________________________
To unsubscribe from the CCPNMR list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPNMR&A=1
########################################################################
To unsubscribe from the CCPNMR list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPNMR&A=1
