NUTS N MR U tility T ransform S oftware Acorn NMR, Inc. Livermore, CA

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

5. Spectral Parameters

6. 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. 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 • 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 • http://www.acornnmr.com/Downloads/NUTSmanual.pdf • Contains command list, table of contents • Help File • Table of Contents • Keyword index • Full text search • Web site • http://www.acornnmr.com/NutsHelp

17. 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

18. 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 • 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. 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. 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 • 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 • 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 • 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 • 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