NUTS Help
Processing magnitude HETCOR data
This is among the simplest 2D experiments, as it requires no phasing. A sample HETCOR data file called small.2d (a 13C-1H spectrum of sucrose) can be downloaded. The resulting 2D plot is shown below.
This page shows how to process this data set with step-by-step explanation. 2 macros are described, one for NUTS-Professional users and one for NUTS-2D users. The goal with these examples is to describe the basic functions to allow users to customize them.
See also descriptions of Links and Macros, magnitude COSY processing, processing Varian and Bruker 2D data.
Users with the Professional version of NUTS can process the data using the following keyboard commands.
Arrayed Mode processing from the command line
| IM | import file called fid (Varian) or ser (Bruker) |
| AR | enter arrayed mode |
| LB | set line broadening to 5 |
| EM | apply exponential window function |
| FT | no phasing is done |
| BC | remove DC and tilt of baseline |
| TD | transpose data |
| MS | apply sine window function (could use EM here, if preferred) |
| ZF | zero-fill (may be repeated if needed) |
| FT | |
| SR | small.2d sample spectrum needs spectrum reverse; other data may or may not need this |
| MC | magnitude calculation |
| BC | remove any DC and tilt in baseline |
| TD | to view data with direct dimension horizontal |
| MH | set minimum height to 10 (good starting guess for contour threshold) |
| SS | set scale |
| IP | intensity plot |
Be sure to save the processed data.
NUTSMACRO Magnitude HETCOR processing using NUTS-Professional ;macro prompts for name of data set ask FileA ga set array_on ; 5 Hz linebroadening in 1st dimension set LB 5 ;link to process in 1st dimension bc em ft bc ;transpose data td ;link to process in 2nd dimension ;uses sine window function, spectrum reverse and magnitude calculation ms ft sr mc bc ; transpose data td set mh 10 ss ip end
Note that NUTS remains in Arrayed Mode at the end of the macro. Be sure to save the final data.
Macro without Arrayed Mode
Before running the macro, import the data with IM. The macro start by prompting for a data file to open – select the translated NUTS file, which always starts with $.
Processing is done one 1 slice at a time, so the sequence of commands is done in a Link, which is repeated for each slice.
Temporary files are written at each stage of processing, so the macro must reset the file names at each stage. Be sure to save the final result.
| NUTSMACRO for magnitude HETCOR ask FileA ga set SL 1 | The macro first asks for the name of the file to be processed, so that the macro does not need to be edited each time it is run.
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| set FileC ft1.2d | The macro writes several temporary files during processing. A file created as output in one step becomes the starting point for the following step, which is why FileA and FileC keep being reset. The output of the first step will be a 2D file called ft1.2d. |
| set LB 5 ga bc em ft bc sc in | The linebroadening for the first (carbon) dimension is set to 5 Hz. The Link reads in each slice, baseline corrects to remove any DC offset of the 2 halves of the FID, applies the exponential multiplication and FT BC applied to the spectrum removes any DC and tilt in the baseline The resulting spectrum is saved as FileC with SC; the IN command increments the file pointers and loops to the beginning of the Link. |
| set FileA ft1.2d set FileC td.2d set SL 1 | Now ft1.2d, the result of the first dimension FT, becomes the starting point for the next processing step, so is set to be FileA. The output of the next step will be a file called td.2d Again, to be safe, the file pointer is set to the first slice. |
| td | TD rotates the matrix so that slices in the other dimension can be read |
| set FileA td.2d set FileC ft2.2d set SL 1 | The next step will operate on td.2d, which is now set to be FileA The result of the second dimension processing, FileC, will be called ft2.2d Again, to be safe, the file pointer is set to the first slice. |
| ga em ft sr mc bc sc in | This Link processes in the second (proton) dimension. Because the digital resolution is poor, we will use the same 5 Hz. linebroadening. Hetcor data from this particular instrument requires a spectrum reverse (SR) command in this dimension. That may need to be removed for data from other sources. MC performs a magnitude calculation and BC removes DC and tilt from the baseline. |
| set FileA ft2.2d ga set SL 1 set FileC final.2d | The data is best viewed with the 13C dimension horizontally, as this is customary and is also the dimension with better digital resolution. So we again reset file names and set the slice pointer. |
| td | Transpose the data |
| set FileA final.2d ga set SL 1 | Load the first slice of the final data set |
| ss set MH 10 ip end | SS normalizes the display scale. It looks through the entire data set to find the largest peak and sets it equal to 100%. Contour levels are defined in the nuts.ini file as mulitples of the Minimum Height (MH) which is expressed as a percent of the largest peak. So SS is needed to get the display correct. MH of 10 means that the first contour is drawn at 10% of the largest peak, appropriate for hetcor data, in which most peaks are similar in height. IP displays a quick intensity plot |
The result should look like this:
This data set can be downloaded, along with macros for processing it.
See also:
Arrayed Mode (NUTS-Pro users only)
Displaying 2D data
description of 2D commands
Processing Varian and Bruker 2D data
Last updated: 3/23/05.