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

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

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

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

Spectral Parameters

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

Processing Parameters

 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

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

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

Subroutines (Zoom, Integration, etc.) Watch status bar 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

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

Help! Manual – 1st 170 pages covers 1D processing Help File Web site 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

 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

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

 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

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

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

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

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

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

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

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

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

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

 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

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

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.

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

 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

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

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

 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

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  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

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

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

Copied as bitmap and expanded Screen resolution is fuzzy

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

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

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

 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

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

 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

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  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

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

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 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

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

The End