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

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Presentation on theme: "NUTS NMR Utility Transform Software Acorn NMR, Inc. Livermore, CA."— Presentation transcript:

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 Edit – Un-Do, copy (Copy options discussed later) Open GA Save SA Print PL Import IM Run Macro RU UnDo ^Z Copy Enhanced Metafile Alt-Shift-E

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

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,, Page Up/Down Base level 2-letter keyboard commands, same as menu commands Does not require 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

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13 Subroutines (Zoom, Integration, etc.) Watch status bar Single-letter keyboard commands Mouse function varies with subroutine Exit with key Dont use buttons!

14 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

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

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 glitchBC 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 1 st - 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 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 1 st region, type 1 select 2 nd region and type 2 Exit Zoom and enter PE routine

25 Phase Region 1 with Left buttonPhase Region 2 with Right button Exit subroutine with key Phase correction is applied to entire spectrum

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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 isnt flat, the baseline isnt 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

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33 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 The scaling factor remains until explicitly changed, regardless of scaling.

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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

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

52 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

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

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55 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

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 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 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 ;set zoom_region #7 to downfield region set zoom_region ; set zoom region #0 to TMS set zoom_region loop 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 ac ; set MH for peak picking set mh 10 pp ; auto-integrate set mh 1 ai an ;save processed file sa end

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61 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


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