GetLineWidthsFromPeakLists.lua

Hi,

Im trying to calculate the error in my peaks ( for RDC). And I tried using this script to extract the line widths from the peaklist. But this message keeps popping up in the terminal window:

Lua> [executing "GetLineWidthsFromPeakLists"]
Selected PeakList I13F_iso_A
[string "GetLineWidthsFromPeakLists"]:275: attempt to index global 't' (a nil value)

And I get no peaklist generated. Could you please advise how I could extract the line widths or calculate the error of the peaks. I have a lot of spectra to work on, and doing it peak by peak is not possible.

Thank you.

Hi Shubhadra
Welcome to the forum. I had a look at the script version at wiki.cara.nmr.ch/ScriptsToGenerateReports. There seems to be a bug on line 275. Just uncomment the whole line (i.e. it should read "-- t.SliceBuffer = {}") and try again please.
Regards
Rochus

Ok, I see that there are some other issues too. I will ask Fred if there is a newer version.
Regards
Rochus

Hi Shubhadra
Fred was so kind to fix the script. Please find it attached. I will also upload it to the wiki.
Regards
Rochus

Attached file: Fixed script

Hi,

Thanks for the new script. It kind of works now, it generates a list of peak number, but no line widths.

Selected PeakList I13F_iso_A
PeakNumber;PeakWidth
1
2
3
4
5

What am I doing wrong? My pearliest is generated using monoscope. And I have updated the script only at the user defined section.

ProjectName="I13F"
SpecId=3 -- enter SpectrumId of Spectrum with PeakList that has BatchList defined (also works with no BatchList)
PeakListId=2 -- edit to be equal to ID of PeakList with BatchList defined
DimTrace=2 -- 1= F1(direct dim), 2= F2 (indirect dim) -- direction of traces whose linewidths are evaluated
DimOrthogonalToTrace=1 -- see above, should be OTHER dimension if DimTrace=1, DimOrthogonalToTrace=2
DeltaPpm = 0.1 -- this is the range of chemical shift around the selected peak to use for lineshape determination
Unit = "Hz" -- unit of the horizontal scale: Hz or ppm

MaxAssymetry = 0.2 -- this parameter excludes residues if their Lineshape is too nonsymmetric at halfheight
-- Assymetry is 2*(LeftHalfWidth-RightHalfWidth/FullWidth)
-- If a reference residue is excluded then this is reported by the script in the Terminal window

--Formatting
sp=";" -- spacer symbol used between datapoints in outputfile

FileSuffix=".csv" -- for output file


Rgds,
Shubhadra

Hi Shubhadra
I forwarded your feedback to Fred who sent me the attached version of the script. Hope this helps.
Regards
Rochus

Attached file: Fixed script

rkeller
Hi Rochus,

It works perfectly now! thank you very much, and please convey my thanks to Fred as well.

Best Regards,
Shubhadra

rkeller
Hi,

The script works fine. I have a small glitch- spectra with negative peaks. I have a few spectra that were processed such that the peaks are all in the negative phase. Could you help? When i run the script, the values reported for peakwidth are all 0.

Thanxs very much!

Rgds,
Shubhadra

The script would need the function for finding maxima modified to search for minima ('<' operator instead of '>' operator) but I suggest that it is much easier to reprocess spectra with 180deg added to zero order phase.
Best, Fred

damberger
Hi,

I re-processed all the spectra. It was indeed much easier. Thanks!

Best Regards,
Shubhadra

Hello,
I am new to cara software, is there any way to generate peak list (nnoesy and cnoesy) from .prot file

Thanks in advance