Re: NMRView peak adjustment

[Bruce Johnson <nmrview@xxxxxxx>]

I have a better script for titrations.  I've got a little more work  
to do on it, but I should have something later this week.

Bruce



On Apr 25, 2007, at 4:21 AM, sette@xxxxxxxxxxx wrote:

> 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