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. 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. More advanced features (not covered here): • 1D: • Inset plots • Text annotation • Interactive baseline correction • Line-fit (deconvolution) • Spectrum simulation from chemical shifts and couplings • Relaxation analysis • Linear prediction • Dual display • Add/subtract • Stacked plots • Math • 2Dprocessing and display

4. Menus(base level of NUTS) • File – import, open, save files; print, run macro • Edit – copy, Un-Do • View • Spectral Parameters – acquisition parameters • Toggle on/off display of peak labels, integrals • Display full spectrum or expanded region • enter Zoom expansion subroutine • Process • Conditions – linebroadening, Minimum height, phase parameters • Window functions • FT • Phase • Baseline correction • Enter integration routine • Peak pick

5. Program Basics • Base level • 2-letter keyboard commands, same as menu commands • Does not require <ENTER> to execute commands • Press left mouse button to display frequency at bottom of screen • 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 • Scale data with scroll bar, < and >, Page Up/Down

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

7. 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

8. 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

9. 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

10. Where are my files? • Working “data” directory – Open and Save commands • “Import” directory – where NUTS looks for foreign files • 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

11. 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

12. Baseline correct the FID – BC to prevent “center glitch”

13. Exponential multiplication • Set linebroadening parameter (LB) and execute with EM • Fourier Transform - FT • Phasing with NUTS • Start with QP – quick automatic phasing • Touch up phasing with one of the manual, mouse-driven phase routines • PH – left and right mouse buttons apply zero-order and 1st- order correction • Set pivot point – before entering PH routine, hold down left mouse button, place cursor and type P • PE – define 2 regions, phase each using expanded display • Switch between regions with 2 mouse buttons • To define the 2 regions, use Zoom – select region, type 1; select 2nd region and type 2; Exit Zoom and enter PE routine • PH and PE are subroutines – exit with <ENTER> key

14. Baseline correction of the spectrum • Distortion can be combination of • DC offset – removed by BC • Linear tilt – removed by BC • Higher order roll - polynomial • QB (Quick polynomial Baseline correction) works in most cases, especially if peaks are sharp and signal-to-noise is good.

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. 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

17. 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 • 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

18. 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

19. Peak Picking - PP Set threshold (minimum height) with cursor and M key or type MH Each PP operation replaces previous peak list Peaks outside current display region are not selected Toggle on/off peak labels with Ctrl-P Labels remain when you open a new data file Peak list is saved with the data

20. 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

21. 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

22. 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

23. 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 • Details can be found in Help file and manual

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

25. Copied as bitmap Screen resolution is fuzzy

26. Enhanced metafile Note that numbers on axis are sharp, not fuzzy When expanded, observe distortion caused by an integer round-off problem

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

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

29. 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

30. 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 also be used to create inset plots • Can create, move, re-size multiple objects

31. 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

32. 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

33. 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

34. 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

35. ; 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 ac ; set MH for peak picking set mh 10 pp ; auto-integrate set mh 1 ai an ;save processed file sa end 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 5 10 0 ;set zoom region #6 for aromatics set zoom_region 6 9 6 ;set zoom_region #7 to downfield region set zoom_region 7 15 10 ; set zoom region #0 to TMS set zoom_region 0 .3 -.3 loop 27 45 pf idc^m isc^m ^f af mf ff bc em ft qp 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

37. More advanced features: • 1D: • Inset plots • Text annotation • Interactive baseline correction • Line-fit (deconvolution) • Spectrum simulation from chemical shifts and couplings • Relaxation analysis • Linear prediction • Dual display • Add/subtract • Stacked plots • Math • 2Dprocessing and display

38. The End