NUTS NMR Utility Transform Software Acorn NMR Inc

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

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

More advanced features (not covered here): 1 D: 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 2 D processing and display

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

Program Basics Base level 2 -letter keyboard commands, same as menu commands Does not require 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

Subroutines (Zoom, Integration, etc. ) Single-letter keyboard commands Mouse function varies with subroutine Exit with key Don’t use buttons! Zoom subroutine Enter Zoom by: 1. View/Zoom menu 2. ZO keyboard command, or 3. Double-click left mouse button 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

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

Help! Manual – 1 st 170 pages covers 1 D 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/Nuts. Help

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

Where are my files? Working “data” directory – Open and Save commands “Import” directory – where NUTS looks 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

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

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

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 1 st- 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 2 nd region and type 2; Exit Zoom and enter PE routine PH and PE are subroutines – exit with key

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.

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

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

Manual integration ID subroutine, exit with 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

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

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

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

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

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

Copying to Word or Power. Point 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

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

Copied as bitmap Screen resolution is fuzzy

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

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

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

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

Putting structures on screen - Meta. Objects (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

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

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

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

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

NUTSMACRO auto-1 D 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 z 0 ^e sz z 5 ; initialize size & position for first IS inset 2 f is xsize. 55, is ysize. 5, is xpos 0, is ypos 0, 2 n, ; display aromatics full scale and create inset z 6 ^e mf isa^m ; initialize size & position for downfiled IS inset 2 f is xsize. 25, is ysize. 1, is xpos 1, is ypos 0, 2 n, ; increase vertical scale 3 x and create inset ac 3 ac z 7 ^e isa^m ; display 10 ->0, adjust scale, PP and enter integration z 5 ^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

More advanced features: 1 D: 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 2 D processing and display

The End