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NUTS N MR U tility T ransform S oftware 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

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slide1

NUTS

NMR Utility Transform Software

Acorn NMR, Inc.

Livermore, CA

slide2

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
slide3

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

slide4

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

slide6

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

slide8

 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
slide9

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
slide11

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
slide13

Subroutines (Zoom, Integration, etc.)

  • Watch status bar
  • Single-letter keyboard commands
  • Mouse function varies with subroutine
  • Exit with <ENTER> key
  • Don’t use buttons!
slide14

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
slide15

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
slide16

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
slide17

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
slide18

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
slide19

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
slide20

Baseline correct the FID – BC

to prevent “center glitch”

DC offset between real and imaginary FIDs

Offset creates glitch

BC removes glitch

slide21

Exponential Multiplication

Set linebroadening parameter (LB) and execute with EM

Improves signal-to-noise at expense of peak broadening

FT

slide22

Phasing with NUTS

    • Start with QP – quick automatic phasing
    • Touch up phasing with one of the manual, mouse-driven phase routines
slide23

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
slide24

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

slide25

Phase Region 1 with Left button

Phase Region 2 with Right button

Exit subroutine with <ENTER> key

Phase correction is applied to entire spectrum

slide27

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
slide28

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

slide29

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

slide30

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
slide31

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

slide33

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.

slide39

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
slide40

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
slide41

Peak Picking - PP

Set threshold (minimum height) with cursor and M key or type MH

slide42

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

slide43

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
slide44

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

slide45

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
slide46

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
slide47

Enhanced metafile – probably fine for most needs

If you shrink the figure, text (axis numbers) may get too small to read

slide48

Copied as bitmap and expanded

Screen resolution is fuzzy

slide49

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

slide50

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

slide51

Enhanced metafile created with macro

Set colors to black, increased font size

When size is reduced, numbers still readable

slide52

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
slide53

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
slide55

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
slide56

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
slide57

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
slide58

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
slide59

; 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 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

slide61

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
  • 2Dprocessing and display