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Re: NMRView peak adjustment


And I suppose it is possible to use this script for titrations as well...

Marco


Citando Bruce Johnson <nmrview@xxxxxxx>:


Here is a modified script that has the linking stuff.  You can  replace
the similar one in peakanalysis.tcl,
or just put this in a file and source it in.


proc Nv_PeakPickFromPeaks {list1 list2 {dataset {}} {lvl {}}} {
    set labels [nv_peak labels $list1]
    if {$dataset == {}} {
         set dataset [lindex [nv_win dataset] 0]
         set lvl [nv_win lvl]
    } else {
        if {$lvl == {}} {
            set lvl [nv_dataset level $dataset]
        }
    }
    foreachpeak peak $list1 {
        if {[Nv_PeakPickAtPeak $list1.$peak $dataset $list2 $lvl 1]  == 1} {
            set n [nv_peak n $list2]
            set newPeak [expr {$n-1}]
            foreach label $labels {
                nv_peak link $list1.$peak.$label $list2.$newPeak.$label
            }
         }
    }
}



On Apr 24, 2007, at 6:22 PM, Bruce Johnson wrote:
Right now it doesn't, but actually I meant for it to work that way. It should link each new peak to the old peak (so they share the same "Resonance"). Then the assignment of the original peak will be shared with the new peak. I'll add this and post a new version of the proc. 

Bruce

On Apr 24, 2007, at 5:41 PM, Andrew Severin wrote:
Does anyone know if with this new command there is an option to have the newly picked peaks also labeled as the former list or if it is just a new list of unlabeled peaks? 

Best,

Andrew


On 4/24/07, Bruce Johnson <nmrview@xxxxxxx> wrote:
Markus, Natalia, et al.

7.0.14 now includes a script which you can run as follows:

Nv_PeakPickFromPeaks list1 list2 dataset lvl

This takes an existing list "list1" and generates a new list "list2"
by picking dataset specified by "dataset" at the threshold set by
"lvl".  If you leave off dataset and lvl it will use the values from
the active spectrum window.

It works by searching within the bounds of each peak in list1 to find
the maximum intensity and then picking a new
peak starting at that position.

Foreach peak in list1 {
    Find position of maximum intensity within the footprint of the
peak in the specified dataset. {
           Pick one peak in the dataset starting at the position of
the maximum
    }
}

I've tested this with a little script (Nv_PeakRandomizeList list1
fraction) which will randomize the position of each peak
a certain fraction of it's current bounds.

It's possible that if two peaks are close to each other it the new
peak will correspond to the position of the wrong peak.

I'll probably also implement something that is closer to what you
asked for, refining the position of a given list, but this was quick
to do, and should be useful.


cheers,


Bruce


On Apr 10, 2007, at 10:57 AM, Markus Voehler wrote:


Natalia
Unfortunately I have not had any response so far.
Markus


On Apr 10, 2007, at 5:01 AM, Natalia Carulla wrote:


Dear Markus,

I would also be interested in knowing about such a tool. I do
quite a lot of HD exchange measurements and such a tool would also
be extremely useful to me. Please let me know if someone answers
you. Thank you very much in advance,

Natàlia

At 22:51 30/03/2007, you wrote:

Bruce

I am looking for a tool to re-fit peak values (bound, width and
volumes) for an existing peak table after changing the level  setting
or reading the peaklist in for a different experiment. This is
commonly the case for titrations or relaxation measurements.  The fit
command appears to re-center the peaks, including a re-
calculation of
the width, but it does not re-adjust the bounds as far as I can
tell.
This feature should be there for relaxation fitting data, but  I can
not find it to adjust single peak lists. (I have posted this
question
some time ago and am still looking for an answer somewhere - Any
input is greatly appreciated.)

Greetings,
Markus


Natàlia Carulla, Ph.D.
ICREA Researcher at Institut de Recerca Biomèdica
Parc Científic de Barcelona
C/ Josep Samitier 1-5
08028 Barcelona
Spain

Tel.: +34-93-4037123
Fax: +34-93-4037126
www.icrea.es
















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@xxxxxxxxxxx
Tel.:          +39-0672594424
Fax:           +39-0672594328