Calculating volumes without refitting peaks

Analysis Version 3
#1

Hi,

I am trying to calculate volumes for my NOESY peaks required for structure calculation.

The program only can calculate volume if I refit the peak first. However in some cases, I don’t want to refit as there is some overlap so it does a poor job for peak position. Is there a way to get the volume without refitting the peak?

Thanks.

#2

I addressed a similar issue the other day at The volume of overlapping peaks - #2 by VickyH. Does that help?
On the whole, if you are fitting overlapped peaks, you should make sure you are using the RG (Refit Peak Group(s)) function so as to fit the peaks together. Sometimes you may need to fit them multiple times to get a good fit, as the starting position does affect it.

Vicky

#3

Yes, group fit is good should the overlap not be too pronounced. Thanks

#4

Do we have a fit where we can change height but not width and position etc…

#5

When coping peak lists we can “fit at position”, so there must be a routine for this somewhere…

#6

I am trying to use this to run the setup xplor_nih structure calculation.

However when I click setup it complains that my NOESY peaklist does not have volumes. Ideally one should just be able to use heights and not require volumes, if possible. Its a lot of potential groups to refit

Thanks,

Joe

#7

Sometimes heights are better, easier to fit and less affected by overlap…

Its an option we should have ideally

regards
Gary

Dr Gary S Thompson NMR Facility Manager
CCPN CoI & Working Group Member
Wellcome Trust Biomolecular NMR Facility
School of Biosciences, Division of Natural Sciences
University of Kent, Canterbury, Kent, England, CT2 7NZ

:phone::01227 82 7117
:email:: g.s.thompson@kent.ac.uk
orchid: ORCID

#8

Hi Joe,

As far as I know Xplor NIH will only use peak volumes.

I will have a look if there is a way round it.

BW,
Eliza

#9

well I could add something to nef pipelines to do maths on frames… e.g.

nef maths --frame xxx --loop yyy {intensity}={volume}

its in the plan!

#10

Well in that case you could always fiddle this one on the command line in CcpNmr Analysis, @JCASSAR.

Open the Python Console with Space,Space and then copy in the following code (obviously replacing the correct PeakList name/PID at the top):

pl = get('PL:noesy.1')
for pk in pl.peaks:
    pk.volume = pk.height

That will simply set your volumes to be the same as your heights and you can go from there.
Copy the PeakList into a new one first if you want to keep this separate from a PeakList with actual volumes.

Vicky

#11

Yes I will try this tomorrow and see if it lets me set up the xplor calculation.

Thanks