1. NMR Utility Transform Software
NUTS
NMR Utility Transform Software
Acorn NMR, Inc.
Livermore, CA

2. Menus – where to find things Program basics
Base level and subroutines
Mouse functions
Keyboard commands
Zoom expansion routine
Scaling data
Getting Help
Manual
Help files
Opening data files
Data and import directories
“Tailer”
Processing
Baseline correction of FID
Exponential multiplication FT
Phasing
Baseline Correction
Integration
Peak Picking
Printing
Copying
Structures on screen
MO subroutine
Customizing NUTS
nuts.ini file
Automation
Command links
Macros

3. Copy Enhanced Metafile Alt-Shift-E
Menus
File – import, open, save files; print, run macro
Run Macro RU
Open GA
Save SA
Edit – Un-Do, copy
(Copy options discussed later)
Import IM
Print PL
Copy Enhanced Metafile Alt-Shift-E
UnDo ^Z

4. Menus, cont. View Spectral Parameters – acquisition parameters
Show Integrals ^I
Toggle on/off display of integrals
Show Peak Labels ^P
Toggle on/off display of peak labels
Show All ^F
Display full spectrum
Show Zoom ^E
Display expanded region
Start Zoom ZO
Enter Zoom expansion subroutine

5. Spectral Parameters

6. Automatic Integrate AI
Menus, cont.
Process
Conditions – linebroadening, Minimum height, phase parameters
Window functions FT
Phase
Baseline correction
Enter integration routine
Peak pick
Phasing >
Baseline Correct BC
Quick Baseline QP
Automatic Integrate AI
Peak Pick PP
Integrate Display ID

7. Processing Parameters

8.  Menus – where to find things Program basics
Base level and subroutines
Mouse functions
Keyboard commands
Zoom expansion routine
Scaling data
Getting Help
Manual
Help files
Opening data files
Data and import directories
“Tailer”
Processing
Baseline correction of FID
Exponential multiplication FT
Phasing
Baseline Correction
Integration
Peak Picking
Printing
Copying
Structures on screen
MO subroutine
Customizing NUTS
nuts.ini file
Automation
Command links
Macros

9. Scale data with scroll bar, < and >, Page Up/Down Base level
Program Basics
Scale data with scroll bar, < and >, Page Up/Down
Base level
2-letter keyboard commands, same as menu commands
Does not require <ENTER> to execute commands

10. Press left mouse button to display frequency at bottom of screen

11. To measure frequency differences (coupling constants):
Press and hold left mouse button
Place vertical cursor on one peak
Click right mouse button (do not release left mouse button)
Move cursor to another peak
Frequency difference displayed at bottom of screen

13. Subroutines (Zoom, Integration, etc.)
Watch status bar
Single-letter keyboard commands
Mouse function varies with subroutine
Exit with <ENTER> key
Don’t use buttons!

14. Zoom subroutine Enter Zoom by: View/Zoom menu ZO keyboard command, or
Double-click left mouse button
<ENTER> to exit Zoom
Ctrl-F for full display, Ctrl-E for expanded display
In Zoom, select zoom region by pressing and holding left mouse button, and wipe across chosen region
Avoid single-click of left mouse button (this selects a region consisting of a single data point)
Right mouse button toggles between full and expanded displays

15. Program basics Getting Help Opening data files Processing Integration
Base level and subroutines
Mouse functions
Keyboard commands
Zoom expansion routine
Scaling data
Getting Help
Manual
Help files
Opening data files
Data and import directories
“Tailer”
Processing
Baseline correction of FID
Exponential multiplication FT
Phasing
Baseline Correction
Integration
Peak Picking
Printing
Copying
Structures on screen
MO subroutine
Customizing NUTS
nuts.ini file
Automation
Command links
Macros

16. Help! Manual – 1st 170 pages covers 1D processing Help File Web site
Contains command list, table of contents
Help File
Table of Contents
Keyword index
Full text search
Web site

17.  Program basics  Getting Help Opening data files Processing
Base level and subroutines
Mouse functions
Keyboard commands
Zoom expansion routine
Scaling data
 Getting Help
Manual
Help files
Opening data files
Data and import directories
“Tailer”
Processing
Baseline correction of FID
Exponential multiplication FT
Phasing
Baseline Correction
Integration
Peak Picking
Printing
Copying
Structures on screen
MO subroutine
Customizing NUTS
nuts.ini file
Automation
Command links
Macros

18. Import data with IM command Save processed data with SA command
Where are my files?
Working “data” directory – Open (GA) and Save (SA) commands
“Import” directory – where NUTS looks for foreign files (IM)
These paths are defined in nuts.ini, but change dynamically as files are opened or saved
WP (Which Path) command – where am I?
Import data with IM command
Save processed data with SA command
What is saved in my file?
Data is saved as you see it on the screen
Integrals, Peak list, etc, saved in file “tailer”
Auto Tailer Read option under the File menu – controls whether or not integrals, etc, are read when a file is opened; can be set in nuts.ini file

19.  Program basics  Getting Help  Opening data files Processing
Base level and subroutines
Mouse functions
Keyboard commands
Zoom expansion routine
Scaling data
 Getting Help
Manual
Help files
 Opening data files
Data and import directories
“Tailer”
Processing
Baseline correction of FID
Exponential multiplication FT
Phasing
Baseline Correction
Integration
Peak Picking
Printing
Copying
Structures on screen
MO subroutine
Customizing NUTS
nuts.ini file
Automation
Command links
Macros

20. Baseline correct the FID – BC to prevent “center glitch”
DC offset between real and imaginary FIDs
Offset creates glitch
BC removes glitch

21. Exponential Multiplication
Set linebroadening parameter (LB) and execute with EM
Improves signal-to-noise at expense of peak broadening FT

22. Phasing with NUTS Start with QP – quick automatic phasing
Touch up phasing with one of the manual, mouse-driven phase routines

23. Manual phasing with mouse
Left and right mouse buttons apply zero-order and 1st- order correction
PH – Do this on full spectrum
Set pivot point – place cursor and type P
Zero-order correction with left button
Adjust peak at pivot point
First-order correction with right button to phase the rest of the spectrum
Exit subroutine with <ENTER> key

24. PE – Phase Expanded, for more close-up view
define 2 regions, phase each using expanded display
Switch between regions with 2 mouse buttons
To define the 2 regions, use Zoom:
select 1st region, type 1
select 2nd region and type 2
Exit Zoom and enter PE routine

25. Exit subroutine with <ENTER> key
Phase Region 1 with Left button
Phase Region 2 with Right button
Exit subroutine with <ENTER> key
Phase correction is applied to entire spectrum

27. Baseline correction of the spectrum Distortion can be combination of
DC offset – removed by BC
Linear tilt – removed by BC
Higher order roll – polynomial
Best method of correction is dependent on characteristics of each spectrum

28. Poor baseline may be most apparent when viewing the integral – if it isn’t flat, the baseline isn’t at zero.

29. More baseline correction features are available; see Help
QB (Quick polynomial Baseline correction) works in most cases, especially if peaks are sharp and signal-to-noise is good.
More baseline correction features are available; see Help

30.  Program basics  Getting Help  Opening data files  Processing
Base level and subroutines
Mouse functions
Keyboard commands
Zoom expansion routine
Scaling data
 Getting Help
Manual
Help files
 Opening data files
Data and import directories
“Tailer”
 Processing
Baseline correction of FID
Exponential multiplication FT
Phasing
Baseline Correction
Integration
Peak Picking
Printing
Copying
Structures on screen
MO subroutine
Customizing NUTS
nuts.ini file
Automation
Command links
Macros

31. Automatic Integration – AI
Integrates all peaks above Minimum Height (MH) threshold
Sets smallest integral to 1.0
If full spectrum is displayed, AI clears previous integrals before integrating
If expanded region is displayed, AI appends integrals to a growing list, allowing successive selected regions to be integrated to create a complete integral list. Scaling is not re-set for successive regions.
Works best for spectrum with well-resolved peaks and no impurities

33. Manual integration ID subroutine, exit with <ENTER>
Scaling the integral vs. scaling the spectrum
Correct the baseline, not the integral!
Define start and stop points for each sub-integral by left mouse clicks
Assign a convenient value to one of the sub-integrals with V key
The scaling factor remains until explicitly changed, regardless of scaling.

39. Whether created automatically or manually:
Integrals remain after exiting ID subroutine
Toggle on/off display of integrals with Ctrl-I (or Tab key)
Integral regions remain defined when you open a new data file
Integral regions are saved with the data
User chooses whether or not integrals are read in when the file is opened at later date

40.  Program basics  Getting Help  Opening data files  Processing
Base level and subroutines
Mouse functions
Keyboard commands
Zoom expansion routine
Scaling data
 Getting Help
Manual
Help files
 Opening data files
Data and import directories
“Tailer”
 Processing
Baseline correction of FID
Exponential multiplication FT
Phasing
Baseline Correction
 Integration
Peak Picking
Printing
Copying
Structures on screen
MO subroutine
Customizing NUTS
nuts.ini file
Automation
Command links
Macros

41. Peak Picking - PP
Set threshold (minimum height) with cursor and M key or type MH

42. Each PP operation replaces previous peak list
Peak list is automatically copied to the clipboard
Peaks outside current display region are not selected
Toggle on/off peak labels with Ctrl-P or from View menu
Labels remain when you open a new data file
Peak list is saved with the data
User chooses whether or not peak labels are read in when the file is opened at later date

43.  Program basics  Getting Help  Opening data files  Processing
Base level and subroutines
Mouse functions
Keyboard commands
Zoom expansion routine
Scaling data
 Getting Help
Manual
Help files
 Opening data files
Data and import directories
“Tailer”
 Processing
Baseline correction of FID
Exponential multiplication FT
Phasing
Baseline Correction
 Integration
 Peak Picking
Printing
Copying
Structures on screen
MO subroutine
Customizing NUTS
nuts.ini file
Automation
Command links
Macros

44. Printing PL
From inside some subroutines, command is just P
WYSIWYG – What You See Is What You Get
Print setup dialog box appears only the first time you print

45.  Program basics  Getting Help  Opening data files  Processing
Base level and subroutines
Mouse functions
Keyboard commands
Zoom expansion routine
Scaling data
 Getting Help
Manual
Help files
 Opening data files
Data and import directories
“Tailer”
 Processing
Baseline correction of FID
Exponential multiplication FT
Phasing
Baseline Correction
 Integration
 Peak Picking
 Printing
Copying
Structures on screen
MO subroutine
Customizing NUTS
nuts.ini file
Automation
Command links
Macros

46. Copying to Word or PowerPoint Options found in the Edit menu
Bitmap
“Metafile” – vector drawing; usually better quality
For historical reasons, there are several variations of Metafiles
Enhanced Metafile works best in most cases
Best choice of parameters depends on starting and final size of image
Details can be found in Help file and manual

47. Enhanced metafile – probably fine for most needs
If you shrink the figure, text (axis numbers) may get too small to read

48. Copied as bitmap and expanded
Screen resolution is fuzzy

49. Enhanced metafile, copied then expanded
Note that numbers on axis are sharp, not fuzzy
When expanded, observe distortion caused by an integer round-off problem by target application
Integer round-off can be minimized by maximizing size of NUTS screen

50. Round-off problem can be avoided
Copied to a file as enhanced metafile with “printer device context, then inserted and expanded
Result is very high resolution

51. Enhanced metafile created with macro
Set colors to black, increased font size
When size is reduced, numbers still readable

52.  Program basics  Getting Help  Opening data files  Processing
Base level and subroutines
Mouse functions
Keyboard commands
Zoom expansion routine
Scaling data
 Getting Help
Manual
Help files
 Opening data files
Data and import directories
“Tailer”
 Processing
Baseline correction of FID
Exponential multiplication FT
Phasing
Baseline Correction
 Integration
 Peak Picking
 Printing
 Copying
Structures on screen
MO subroutine
Customizing NUTS
nuts.ini file
Automation
Command links
Macros

53. Putting structures on screen - MetaObjects (MO) subroutine
Paste structure from clipboard or import Windows Metafile (.wmf)
If imported from a file, a “pointer” to that file will be saved when
the data file is saved, so can be recalled later
Can create, move, re-size multiple objects
Can also be used to create inset plots, but Inset Plot routine (IS) usually gives better results

55.  Program basics  Getting Help  Opening data files  Processing
Base level and subroutines
Mouse functions
Keyboard commands
Zoom expansion routine
Scaling data
 Getting Help
Manual
Help files
 Opening data files
Data and import directories
“Tailer”
 Processing
Baseline correction of FID
Exponential multiplication FT
Phasing
Baseline Correction
 Integration
 Peak Picking
 Printing
 Copying
 Structures on screen
MO subroutine
Customizing NUTS
nuts.ini file
Automation
Command links
Macros

56. Nuts.ini – text file read by NUTS when it is launched
Contains user preferences for:
Import and data directories
Automatically read “tailer” data when opening a file
Default LB value
Automatic peak pick when MH is set with cursor
Un-Do on/off
Fonts – integral, peak label
Define zoom regions (eg, 0-10 ppm for plots)
Pre-defined command links and macros
Colors
Margins
Includes description of each parameter and how to set it

57.  Program basics  Getting Help  Opening data files  Processing
Base level and subroutines
Mouse functions
Keyboard commands
Zoom expansion routine
Scaling data
 Getting Help
Manual
Help files
 Opening data files
Data and import directories
“Tailer”
 Processing
Baseline correction of FID
Exponential multiplication FT
Phasing
Baseline Correction
 Integration
 Peak Picking
 Printing
 Copying
 Structures on screen
MO subroutine
 Customizing NUTS
nuts.ini file
Automation
Command links
Macros

58. Command “links” – frequently used string of commands
Automation
Command “links” – frequently used string of commands
LI – display link definitions (set by nuts.ini)
A# (where # = 1, 2, …) executes the corresponding Link
Example for routine processing
bc em ft qp
Macros – text files containing NUTS commands
More flexible and powerful than Links

59. NUTSMACRO auto-1D batch processing
;FT, auto-phase and baseline correct
set lb 0.3
; set zoom region #5 to 10->0 ppm, for plotting
set zoom_region
;set zoom region #6 for aromatics
set zoom_region 6 9 6
;set zoom_region #7 to downfield region
set zoom_region
; set zoom region #0 to TMS
set zoom_region
loop 27 45
pf idc^m isc^m ^f af mf
ff bc ft ap it em ft ps
z0 ^e sz z5
; initialize size & position for first IS inset 2f
is xsize .55,
is ysize .5,
is xpos 0,
is ypos 0,
2n,
; display aromatics full scale and create inset
z6 ^e mf isa^m
; initialize size & position for downfiled IS inset 2f
is xsize .25,
is ysize .1,
is xpos 1,
is ypos 0,
2n,
; increase vertical scale 3x and create inset
set ac 3 ac
z7 ^e isa^m
; display 10->0, adjust scale, PP and enter integration
z5 ^e
set ac 0.1
; set MH for peak picking
set mh 10 pp
; auto-integrate
set mh 1 ai an
;save processed file sa
end

61. 2D processing and display
Advanced Features
1D:
Inset plots
Text annotation
Interactive baseline correction
Line-fit (deconvolution)
Spectrum simulation from chemical shifts and couplings
Linear prediction
Dual display
Add/subtract
Stacked plots
Math
2D processing and display

62. The End