Transcript Document

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):
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
2D 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 <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
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:
1. View/Zoom menu
2. ZO keyboard command, or
3. 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
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
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
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 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
 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 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
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 <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
 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 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
Enhanced metafile – probably fine for most needs
If you shrink the figure, text (axis numbers) may get too small to read
7
6
5
4
3
2
1
0
PPM
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
6
5
Round-off problem can be avoided
Copied to a file as enhanced metafile with
“printer device context”, then inserted
Result is very high resolution
6
5
4
Enhanced metafile created with macro
Set colors to black, increased font size
When size is reduced, numbers still readable
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6
5
4
3
2
1
0 PPM
 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 - 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
 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-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
; 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
13.0
12.5
12.0
11.5
11.0
8.5
2.480
3.846
6.681
6.660
6.590
7.264
13.5
10.5
P PM
8.0
7.5
7.0
6.5
PPM
12.73
3.80
2.45
1.17
0.89
8
6
1.20
1.21
1.22
4
1.45
1.33
2
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
2D processing and display
The End