Hi!
I am currently integrating spectra using bins. I have manually integrated the regions by 0.5 ppm bins. I did it on one spectrum and then could save this file and then import the defined integral regions on other spectra.
I now want to do smaller bin widths but not like I did before. I want to know if Ican define integral regions in one go like: Integrate from 0 to 10 ppm with a widht of 0.04 ppm.
I tried to export the former file and change it in editor or excel but I had problems with how the columns and rows looked like, it didn't match with how the format should be in/for TopSpin.
Has anyone done this before and could help me out?
Thank you!
Dear colleague,
it should be no problem to set up the "intrng" text file with the desired regions manually if you follow the format requirements of the software. I noticed that this information is difficult to find in the actual software documentation. Therefore I have added a copy taken from a very early version but this should still be vaild.
Good Luck!
Here is a very easy way to do this, using our friend, ChatGPT.
Enter this text into the prompt:
I need to produce a text file in a specific manner. For context, first line is a header line with the headings "low field" "high field" "bias" "slope" "comment", each heading title separated by two spaces. the lines of data will start with a value of 10 for "low field", then "high field" is to be "low field" subtract 0.04. "bias" and "slope" should have values of "-0.0", and the comment should say "# for region X", where "X" is the data line number the separators between values is two spaces. please produce the text that I need for this file for data lines that go from 10 down to 0, where the low field value in each line is the value of the high field from the previous line. Please include the following text as the first line: "A 1.0 #regions in PPM"
Then you can copy-paste this into a file that you will read in using TopSpin command rmisc intrng
You can change the parameters in the above text to get the desired output. This one fits what you asked for (bins from 0 to 10 ppm in 0.04 ppm steps).
edit: I tested this using "subtract 0.4" which is 25 regions. if you want the 250 regions using 0.04 ppm bins, you may need to additionally prompt GPT with "please produce the whole file from 10 down to 0", and then click "continue generating" a few times until it's finished.
You could also try getting it to produce a python code to generate the file.
Hi, you are a savior. Yes I noticed that you have to include that it should go down from 10 to 0. Thanks a lot!
A small question: A txt file should work in TopSpin, right?
You will save the file in the directory /exp/stan/nmr/lists/intrng It's just a text file, but with no extension.
So you take that output from ChatGPT and copy it into a text editor. Then save the file, but remove the .txt extension if it applies it.
Dear Esswarijah,
for more "old school people" the problem can be solved by use of a bit of Excel/gsheet/libreoffice...
0.04
10.0 X2-$X$1 0.0 0.0 #integral1
X1-$X$1 X3-$X$1 0.0 0.0 #integral2
... ... ... ... ...
If you expand the colums down to 0.0 in the first column with the mouse you can export this file as a text file and place it in the intrng directory of topsin ... maybe you'll have to fiddle "a bit" with the numer of "spaces" between columns - check this in existing integral filed.
Alfred
P.S. for me (as old-school scientis) this was simpler than writing a "short story" telling ChatGPT what I need .... :-)
Hi Alfred,
thank you for your suggestion, that is how I did it too initially :) I also feel this is simpler. Especially when you are working with small integral regions, chatgpt isn't able to print that many lines.
When doing it like you suggested I had to arrange the rows/cols a bit, but unfortunately it still seems not to be in the right format.
..hmm
- I exported/stored the enclosed Excel File (created as described in my previous post) in csv Format by use of Excel (IntegralRegin.csv).
- I opened this csv File in a text editor and replaced each comma by TWO spaces and I added the first two lines copied form another integral file stored by topspin (wmisc intrng).
- Finally I stored the modified csv-file in the integral directory of topspin. The resulting (text) file "BinTest" you'll find attached.
- I read it in into topspin by use of "rmisc intrng BinTest". The result looks good to me (see bmp picture attached).
Hope this helps
Alfred
As Alfred Ross suggested, there is a simple solution, see attached file, generated with Excel within a few minutes,
then data copied to text editor to create the final format.
Important: no commas, decimal points are required
no tabs, use three spaces to separate values instead
it works!
Note: from line 33 on, there are not three spaced between values, this does no longer work.
Update to my previous post: There needn't be three spaces, one or two work fine as well...
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