NUTS N MR U tility T ransform S oftware Acorn NMR, Inc. Livermore, CA
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Transcript of NUTS N MR U tility T ransform S oftware Acorn NMR, Inc. Livermore, CA
Menus – where to find thingsProgram basics
Base level and subroutinesMouse functionsKeyboard commandsZoom expansion routineScaling data
Getting HelpManualHelp files
Opening data filesData and import directories“Tailer”
ProcessingBaseline correction of FIDExponential multiplicationFTPhasingBaseline Correction
Integration Peak Picking
PrintingCopying Structures on screen
MO subroutineCustomizing NUTS
nuts.ini fileAutomation
Command linksMacros
MenusFile – import, open, save files; print, run macro
Edit – Un-Do, copy (Copy options discussed later)
Open GASave SA
Print PL
Import IM
Run Macro RU
UnDo ^Z
Copy Enhanced Metafile Alt-Shift-E
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 subroutineShow Peak Labels ^P
Toggle on/off display of peak labels
Show Zoom ^E
Display expanded region
Menus, cont.Process
Conditions – linebroadening, Minimum height, phase parametersWindow functionsFTPhaseBaseline correctionEnter integration routinePeak pick
Phasing >
Baseline Correct BC
Quick Baseline QP
Automatic Integrate AIPeak Pick PPIntegrate Display ID
Menus – where to find thingsProgram basics
Base level and subroutinesMouse functionsKeyboard commandsZoom expansion routineScaling data
Getting HelpManualHelp files
Opening data filesData and import directories“Tailer”
ProcessingBaseline correction of FIDExponential multiplicationFTPhasingBaseline Correction
Integration Peak Picking
PrintingCopying Structures on screen
MO subroutineCustomizing NUTS
nuts.ini fileAutomation
Command linksMacros
Program Basics
Scale data with scroll bar, < and >, Page Up/Down
Base level
2-letter keyboard commands, same as menu commandsDoes not require <ENTER> to execute commands
To measure frequency differences (coupling constants):Press and hold left mouse buttonPlace vertical cursor on one peakClick right mouse button (do not release left mouse button)Move cursor to another peakFrequency difference displayed at bottom of screen
Subroutines (Zoom, Integration, etc.)Watch status barSingle-letter keyboard commandsMouse function varies with subroutineExit with <ENTER> keyDon’t use buttons!
Zoom subroutineEnter Zoom by:
1. View/Zoom menu2. ZO keyboard command, or3. 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 basicsBase level and subroutinesMouse functionsKeyboard commandsZoom expansion routineScaling data
Getting HelpManualHelp files
Opening data filesData and import directories“Tailer”
ProcessingBaseline correction of FIDExponential multiplicationFTPhasingBaseline Correction
IntegrationPeak PickingPrintingCopying
Structures on screenMO subroutine
Customizing NUTS nuts.ini file
AutomationCommand linksMacros
Manual – 1st 170 pages covers 1D processing http://www.acornnmr.com/Downloads/NUTSmanual.pdfContains command list, table of contents
Help FileTable of ContentsKeyword indexFull text search
Web sitehttp://www.acornnmr.com/NutsHelp
Help!
Program basicsBase level and subroutinesMouse functionsKeyboard commandsZoom expansion routineScaling data
Getting HelpManualHelp files
Opening data filesData and import directories“Tailer”
ProcessingBaseline correction of FIDExponential multiplicationFTPhasingBaseline Correction
IntegrationPeak PickingPrintingCopying
Structures on screenMO subroutine
Customizing NUTS nuts.ini file
AutomationCommand linksMacros
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 screenIntegrals, 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 basicsBase level and subroutinesMouse functionsKeyboard commandsZoom expansion routineScaling data
Getting HelpManualHelp files
Opening data filesData and import directories“Tailer”
ProcessingBaseline correction of FIDExponential multiplicationFTPhasingBaseline Correction
IntegrationPeak PickingPrintingCopying
Structures on screenMO subroutine
Customizing NUTS nuts.ini file
AutomationCommand linksMacros
Baseline correct the FID – BCto prevent “center glitch”
DC offset between real and imaginary FIDs
Offset creates glitch BC removes glitch
Exponential MultiplicationSet linebroadening parameter (LB) and execute with EMImproves signal-to-noise at expense of peak broadening
FT
Phasing with NUTSStart with QP – quick automatic phasingTouch 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 spectrumSet pivot point – place cursor and type P
Zero-order correction with left buttonAdjust 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 viewdefine 2 regions, phase each using expanded displaySwitch 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
Phase Region 1 with Left button Phase Region 2 with Right button
Exit subroutine with <ENTER> keyPhase correction is applied to entire spectrum
Baseline correction of the spectrum
Distortion can be combination of DC offset – removed by BCLinear tilt – removed by BCHigher 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.
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 basicsBase level and subroutinesMouse functionsKeyboard commandsZoom expansion routineScaling data
Getting HelpManualHelp files
Opening data filesData and import directories“Tailer”
ProcessingBaseline correction of FIDExponential multiplicationFTPhasingBaseline Correction
IntegrationPeak PickingPrintingCopying
Structures on screenMO subroutine
Customizing NUTS nuts.ini file
AutomationCommand linksMacros
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 subroutineToggle 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 basicsBase level and subroutinesMouse functionsKeyboard commandsZoom expansion routineScaling data
Getting HelpManualHelp files
Opening data filesData and import directories“Tailer”
ProcessingBaseline correction of FIDExponential multiplicationFTPhasingBaseline Correction
IntegrationPeak PickingPrintingCopying
Structures on screenMO subroutine Customizing NUTS nuts.ini file
AutomationCommand linksMacros
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 basicsBase level and subroutinesMouse functionsKeyboard commandsZoom expansion routineScaling data
Getting HelpManualHelp files
Opening data filesData and import directories“Tailer”
ProcessingBaseline correction of FIDExponential multiplicationFTPhasingBaseline Correction
Integration Peak PickingPrintingCopying
Structures on screenMO subroutine
Customizing NUTS nuts.ini file
AutomationCommand linksMacros
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 basicsBase level and subroutinesMouse functionsKeyboard commandsZoom expansion routineScaling data
Getting HelpManualHelp files
Opening data filesData and import directories“Tailer”
ProcessingBaseline correction of FIDExponential multiplicationFTPhasingBaseline Correction
Integration Peak Picking PrintingCopying
Structures on screenMO subroutine
Customizing NUTS nuts.ini file
AutomationCommand linksMacros
Copying to Word or PowerPoint
Options found in the Edit menuBitmap“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
7 6 5 4 3 2 1 0 PPM
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
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
7 6 5 4 3 2 1 0 PPM
Round-off problem can be avoidedCopied to a file as enhanced metafile with “printer device context, then inserted and expandedResult is very high resolution
7 6 5 4 3 2 1 0 PPM
Enhanced metafile created with macroSet colors to black, increased font sizeWhen size is reduced, numbers still readable
Program basicsBase level and subroutinesMouse functionsKeyboard commandsZoom expansion routineScaling data
Getting HelpManualHelp files
Opening data filesData and import directories“Tailer”
ProcessingBaseline correction of FIDExponential multiplicationFTPhasingBaseline Correction
Integration Peak Picking Printing Copying
Structures on screenMO subroutine
Customizing NUTS nuts.ini file
AutomationCommand linksMacros
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 basicsBase level and subroutinesMouse functionsKeyboard commandsZoom expansion routineScaling data
Getting HelpManualHelp files
Opening data filesData and import directories“Tailer”
ProcessingBaseline correction of FIDExponential multiplicationFTPhasingBaseline Correction
Integration Peak Picking Printing Copying
Structures on screenMO subroutine
Customizing NUTS nuts.ini file
AutomationCommand linksMacros
Nuts.ini – text file read by NUTS when it is launched
Contains user preferences for:Import and data directoriesAutomatically read “tailer” data when opening a fileDefault LB valueAutomatic peak pick when MH is set with cursorUn-Do on/offFonts – integral, peak labelDefine zoom regions (eg, 0-10 ppm for plots)Pre-defined command links and macrosColorsMargins
Includes description of each parameter and how to set it
Program basicsBase level and subroutinesMouse functionsKeyboard commandsZoom expansion routineScaling data
Getting HelpManualHelp files
Opening data filesData and import directories“Tailer”
ProcessingBaseline correction of FIDExponential multiplicationFTPhasingBaseline Correction
Integration Peak Picking Printing Copying
Structures on screenMO subroutine
Customizing NUTS nuts.ini file
AutomationCommand linksMacros
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 processingbc em ft qp
Macros – text files containing NUTS commandsMore flexible and powerful than Links
NUTSMACRO auto-1D batch processing;FT, auto-phase and baseline correctset lb 0.3; set zoom region #5 to 10->0 ppm, for plottingset zoom_region 5 10 0
;set zoom region #6 for aromaticsset zoom_region 6 9 6
;set zoom_region #7 to downfield regionset zoom_region 7 15 10
; set zoom region #0 to TMSset zoom_region 0 .3 -.3
loop 27 45pf idc^m isc^m ^f af mfff bc ft ap it em ft psz0 ^e sz z5
; initialize size & position for first IS inset2fis xsize .55,is ysize .5,is xpos 0,is ypos 0,2n,; display aromatics full scale and create insetz6 ^e mf isa^m
; initialize size & position for downfiled IS inset2fis xsize .25,is ysize .1,is xpos 1,is ypos 0,2n,
; increase vertical scale 3x and create insetset ac 3acz7 ^e isa^m
; display 10->0, adjust scale, PP and enter integrationz5 ^eset ac 0.1ac
; set MH for peak pickingset mh 10pp
; auto-integrateset mh 1aian
;save processed filesaend
8 6 4 2 PPM
7.8
25
7.7
60
4.1
45
4.1
33
3.9
81
3.3
15
2.5
10
2.5
06
2.5
01
2.4
96
1.1
45
1.1
27
1.1
09
0.0
00
0.91
4.12
2.00 2.06 2.00
1.03
6.04
4.00
8.5 8.0 7.5 7.0 6.5 PPM
14.5 14.0 13.5 13.0 12.5 12.0 11.5 11.0 PPM
Advanced Features
1D:Inset plotsText annotationInteractive baseline correctionLine-fit (deconvolution)Spectrum simulation from chemical shifts and couplingsLinear predictionDual displayAdd/subtractStacked plotsMath
2D processing and display