Chapter 2
For
instructions on SpecMan installation, please refer to ‘The Release Notes’ or
‘specmanPCreadme’ file supplied with the program.
SpecMan
and SpecManPlus are copy protected by the Spectrum Research Licensing
System. This licensing system allows
SpecMan/SpecManPlus to run only on the computer for which it was sold. To obtain a valid license file (license.dat)
in order to activate SpecMan, please provide Spectrum Research with the Product
ID from your PC system. To retrieve the
Product ID, right-click on the “My Computer” icon on your Windows Desktop. Choose “Properties” from the menu that pops
up, and your Product ID will be listed in the “Registered To:” section (For
example: 02658-OEM-2564589-12458). Once
you have received the trial license file, place a copy of it in the
C:\Spectrum2001\SpecMan directory.
When
the trial licensing time is nearing expiration, SpecMan will display a dialog
box indicating the number of days remaining for the license. Please contact Spectrum Research for a
renewal at that time.
To
launch the SpecMan program, click on the specman.exe icon from the File Manager
or Windows Explorer (By default, SpecMan is installed into
C:\Spectrum2001\SpecMan). The program
starts with a Main Graphics Window
that has a menu bar and status bar.
When
SpecMan has been initiated, it attempts to locate the specman.ini file in the
SpecMan directory. This file defines
many of the initial settings for SpecMan, such as window sizes, default colors,
font sizes, etc. (please review the ‘Edit - Initialization File’ section for
more information).
If
the user is new to Microsoft Windows or Windowing systems in general, please
read this section before using SpecMan to become acquainted with the SpecMan
interface.
When
SpecMan is first initiated, a window will appear with "SpecMan, version
2.4, (C) Spectrum Research, LLC." on the top. The area where this text appears is referred to as the ‘Title
Bar.’ By pressing the left mouse button
while the cursor is on the title bar, and then moving the mouse, the window
will move. Releasing the mouse button
will stop the window from moving. This
combination (pressing the mouse button, moving the mouse, and then releasing
the mouse) is known as ‘Dragging.’
Position the cursor so that it is over the word ‘File’, located
immediately below the title bar. Now
press and then immediately release the left mouse button. This procedure (pressing a mouse button and
then releasing without moving the mouse) is known as ‘Clicking.’ The item that was clicked on was the ‘Menu
Bar.’ The menu bar consists of the
‘File’ menu, the ‘Edit’ menu, the ‘Display’ menu, the ‘Analysis’ menu and the
‘Help’ menu. After clicking on the
‘File’ menu, a pulldown tab will appear consisting of additional menu items
such as ‘Open Spectrum,’ ‘Open Multiple Spectra,’ ‘Open Molecule,’ ‘Save
Molecule,’ etc. Menu items are the
primary way that the SpecMan user can communicate with SpecMan.
In
addition to the menu items on each pulldown menu, there are ‘Separator’ lines
such as the line that appears above ‘Quit’ on the File menu. Its purpose is solely to make the menu
easier to read. Click on the ‘Display’
menu and notice that the ‘Units’ menu item has a right pointing triangle after
its text. This type of menu item is
known as a pullright menu. Click the
mouse on the ‘Units’ menu item and another group of menu items will appear to
the right of the 'Units' menu item.
This pullright feature is used to group related menu items together,
reducing the size of the main pulldowns.
Click on the "Display" menu and then click on the "Peaks
Tables" pullright. These three
menu items are known as "Toggles".
Toggles have two states:
"Off" (also known as "Deselected" or
"Deactivated"), and "On" (also known as "Selected"
or "Activated"). Click on the
"1D..." toggle and another window will pop up with the title of
"1D Peaks Table". Click on
the "Analysis" menu and the "Peaks Tables" pullright again
and now there is a check mark next to the "1D..." toggle. This means
that the toggle is now "On".
Click on the toggle again to turn it "Off" and the "1D Peaks Table" will disappear.
Position
the mouse cursor over the frame that surrounds the entire SpecMan window. Drag the mouse to change the size of the
SpecMan window. All sides of the
SpecMan window can be moved to size the window. The field below the SpecMan
Toolbar is known as the "Graphics Viewport". This is where information about Spectra is
displayed. At the bottom of the Graphics
Viewport is the "Status Bar" that lists information about what is
currently happening in SpecMan. It will
notify the user if the user is trying to do a task that SpecMan isn't prepared
to do, and it will also give the user hints about using SpecMan.
Click
on "Open Spectrum" from the "File" menu and a window will
appear with the title of "Open".
This type of window is known as a dialog box. While a dialog box is displayed, the user must interact with it
before continuing with other areas of SpecMan.
The dialog box that is currently displayed is referred to as the
"File Browse Dialog" and it is used to specify a file to be
opened. The "OK" button on
the bottom of the dialog box is used to accept the input file. When opening a spectral data file, the user
needs to input the format type for the spectral data (i.e. Varian, Bruker,
JEOL, etc.). The "Files of
Type:" drop down box near the bottom of the file browse dialog is used for
this purpose. Varian, Bruker and JEOL
sample data have been supplied with the SpecMan program, so select the file
type as "Varian" and then locate the sample Varian data files in the
C:\Spectrum2001\Data\Q-2 folder. The
user can ascend and descend the directory structure by double clicking on a
directory name from the list. (A “double
click” is two clicks followed in rapid succession.) After changing to the C:\Spectrum2001\Data\Q-2\HMQC folder, click
on the 'phasefile' file and then select 'OK'.
The HMQC spectrum will now be displayed in the Spectral window.
To
the right of the main SpecMan window is a window titled
"Threshold." This is known as
a "Palette." Palettes are
similar to dialog boxes, however the user can interact with them and with the
main SpecMan window at the same time.
The "Threshold" palette is used to control the display of 2D spectral contours. Be warned,
however, that changing the threshold on a large matrix can require a few
minutes to compute, depending on how fast the computer is. In the "Threshold" palette, there
are 4 controls known as "Sliders".
The user can drag a slider bar to the left and right to raise and lower
its value. Also, to the right of the
"Threshold" slider is a text field that contains the currently
displayed threshold value. New values
can be entered into this filed and then accepted by clicking the
"Update" button.
Once
a spectrum is open, the user can use most of the other menu items that were
previously disabled (i.e. gray and inactive).
The
toolbar appears between the menubar and the Main Graphical Window, and it
contains icons that represent commonly used menu items. By clicking on one of the icons, the same
action that occurs when the user selects the corresponding menubar item will
happen. If the user holds the cursor
steady over a menubar item, a short description of that item will be displayed.
The
following menu items have associated toolbar icons:
File/Open 
Edit/Undo
Display/Threshold 
Display/1D Slice
Analysis/Crosshair
Cursor 
Display/Set Active
Viewport
Display/Associate
Reference Spectra 
Display/Set
Labels
Display/Increase
Zoom 
Display/Decrease
Zoom
Analysis/Previous
Zoom 
Analysis/Reset
Zoom
Analysis/Pick
Peaks Automatically/1D 
Analysis/Pick
Peaks Automatically/2D
Analysis/Pick Peaks
Automatically/3D 
Analysis/Show
Peaks
Analysis/Move Peaks 
Analysis/Merge
Peaks
Analysis/Add
Peaks Manually/Singlet 
Analysis/Add
Peaks Manually/Multiplet
Analysis/Add
Peaks Manually/Without Refine
Analysis/Add Peaks Manually/Grid Location
Analysis/Remove
Peaks 
Analysis/Annotate
Peaks
Help/Contents
Chapter 3
This
chapter helps the user navigate SpecMan’s File Menu and its features, as well
as relevant main concepts and principles.
To
analyze spectra in SpecMan, first transfer the data files to the computer that
SpecMan is located on, or alternately, the files can be accessed via a network. However, this latter option limits the speed
of SpecMan to the speed of the network connection. The file formats that SpecMan can import are listed as follows:
·
Bruker: 1rr and procs files for 1D spectra; 2rr, procs and proc2s files for 2D spectra.
·
Varian: phasefile and procpar files.
·
JEOL: *.als for Alice, *.nmd for Alpha, *.bin and
*.hdr for Generic, *.nmdata for Lambda and *.1 for
Delta.
·
NMRPipe: *.ft2
files.
·
NMRCompass: *.spc files.
·
Galactic: *.spc files.
·
JCamp: *.dx files.
·
Felix: *.mat files.
·
FiveAsh Database Management
Handbook:
*.dat files.
·
Chemical Shift Database: *.sdb files.
·
Chemical Concepts Database: *.jdx files.
·
Custom Spectral Database: *.spd files.
·
Triad: *.nmr and *.nmr_h files.
·
Spectrum Research: *.exp files.
·
Mass Spec (HPLC-MS) and UV (HPLC-UV): *.bin files.
·
NUTS: *.xd files (x is the dimensionality).
Once
the appropriate files have been transferred from a spectrometer or from a 3rd
party processing software program, open a spectrum in SpecMan by
selecting ‘Open a Spectrum’ from the File menu. Upon selecting this option, the following ‘File Browse’ dialog box is displayed:
Navigate
the browser by double clicking a directory to change to it and double clicking
a filename to select it and select the proper input file format from the File
Type drop down menu. The user can
modify the specman.ini and specmanpersonal.ini files to set the default format
type to Bruker, Varian, JEOL, NMRPipe, etc., when working primarily with data
of the same format.
If
this is the first time that a spectrum is being read by SpecMan, the program
will generate a contour file (please note that this can be time consuming on
large, complex matrices, over a network, or on slow computers). After the contours have been generated, they
are stored in a *.con file with the
same root name as the name of the spectrum.
SpecMan reads this file when the spectrum is re-loaded in the future, so
that the contours don’t have to be regenerated. When transferring files that were previously analyzed by SpecMan,
also copy the contour file so that the contours will not have to be
regenerated.
SpecMan
allows simultaneous display of several spectra with multiple views. This is done by selecting, ‘Open Multiple
Spectra’ from the File menu. The
multiple spectra can include a combination of 1D, 2D and 3D experiments of the same
sample to enable mixing and matching of any combination of 1D, 2D and 3D experiments for display.
The user can also save all of the associated multiple spectral data as
one file list and then open it to display the spectra. When ‘Open Multiple Spectra’ is selected,
the following dialog box will appear:
Click
on ‘Add’ and then select the initial spectral file from the following dialog
box:
To
add additional spectra, re-select ‘Add,’ and then repeat until all of the
desired spectra have been added. As
files are selected in the Open file browser, the list of selected files will be
displayed in the Open Multiple Spectra dialog box, as shown below:
Once
the desired spectra have been chosen, click 'OK' in the Open Multiple Spectra
dialog box to read and display the selected multiple spectra.
At
any time, only one spectrum is kept as the active spectrum and the rest are
treated as passive spectra. Therefore,
some of the immediate menu commands are applicable only to the active
spectrum. The user can make a passive
spectrum active by using the Set Active command. The user can also delete a selected file from the Open Multiple
Spectra dialog box by clicking on the filename and then clicking ‘Delete.’ This delete will only delete the file from
the list of multiple files and will not delete the original copy from the disk.
Multiple
2D spectra (HMQC & HMBC) are shown in the following:
When
working with multiple spectra of the same molecule, it can be convenient to tie specific axes of
spectra together. This is accomplished
through the Tie Views option in the Display menu. When this option is chosen, the following Tie Manager dialog box
is displayed:
The
Tie All 1D option ties the X axes of all open 1D spectra. The Tie All 2D option ties the X axes and Y axes of all open 2D and higher spectra. The Untie All option removes all tying from all
open spectra. To tie the axes of two
specific spectra, select the First Spectrum and Second Spectrum text boxes to
specify the desired spectra to tie.
Then, click on either X&X to tie both of the X axes, or select
Y&X to tie one of each axis. Note
that in the tied mode the cross-hair cursors of each spectrum are also tied
together so that they move together when you scroll in either spectrum. Then, select OK and the spectra will be tied
as in the following (shown with the 1D reference grid lines turned off):
In
the above view the HMQC spectrum is tied to the HMBC spectrum. In a similar manner, the user can also use
this feature for analysis of multiple 1D spectra with tied frequency axes. This will enable the user to align common
peaks between the different 1D spectra and identify multiplicities in Carbon
data. Also this view mode can be used
for setting the common spectral reference between Carbon and DEPT data. The user can also perform 1D peak picking
and overlay the picked peaks on any related spectrum for comparison in this
multiple spectral view.
This
function is used to display a molecule with or without its corresponding
assignments. The user can import *.mdl,
*.mol or *.sdf files into SpecMan and open them as shown in the following
dialog box:
Open
Molecule also enables the user to open multiple molecules. Click on Open
Molecule to open one molecule, and then click on Open Molecule again to select
a second molecule. Repeat until the
desired amount of structures have been opened:
This function is used to save a molecule (with assignments)
as a *.mdl, *.mol or *.sdf file. Select
‘Save a Molecule’ from the File menu and the following dialog box will appear:
Select the desired format and type in a filename to save the
structure file. Note that the
assignments will be appended to the end of the structure file.
This
function is used for creation of a custom spectral database. The user can create a database from any type
of vendor data that can be imported by SpecMan, and can then search through
individual spectra, structures, peaks tables and assignment tables. More details regarding the features of
assignment tables generated by NMR-SAMS can be found in the Display Menu of
this document.
To
create a database, first select Manage Custom Database from the Edit menu, and
the following window will appear:
To
create the database in the current directory, type a name in the text box next
to Database Filename. However, to
create the database in a different directory, select the Browse button next to
the Database Filename text box. After
selecting the new directory, type in the name of the database and the *.spd
filename will be added automatically.
After
defining the database name, the next step is to add the entries. Each entry can consist of spectra, molecular
structures, peaks tables, and assignment tables. Except for the spectrum, the other entries are optional. If for instance a peaks table or assignment
table is not designated, then the peaks table or assignment table window will
not be displayed. When 'Add' is
selected, the following open file selector will appear to aid the user in
finding a 1D or 2D spectra:
Once
the correct spectrum file has been selected, the path name corresponding to the
chosen spectrum will be highlighted in the Spectra text box on the Manage
Custom Database window. Select browse
next to the Molecule text box in order to select the molecule (*.mdl , *.sdf
and *.mol files from NMR-SAMS, along with other *.mol structures created by
sketching programs such as ChemDraw, ISIS, etc.). Then type in the name of the molecule, and select browse next to
the Peaks Table text box. This will
allow the user to select the desired peaks table (with extension *.pks). Then, select browse next to the Assignment Table
text box and select the corresponding assignment table (with extension *.rst). The completed initial entry will appear as
follows:
To
enter additional entries, click Add and repeat the above-mentioned
process. All of the information is
stored in memory until 'Create' is clicked.
When 'Create' is clicked, the information is written to an *.spd
file. If the user selects Cancel before
Create, all entered information will be lost.
The user's custom database has now been created, and can be accessed by
selecting Open a Spectrum under the File menu.
Be sure to select the type of file as *.spd, and the following windows
will appear:
The
Database Browser is used to browse through and search for entries in the
database. The browser contains the name
of the current spectrum; a slide bar for sliding through the individual entries
in the database; the number of entries in the database, and the current entry
being displayed; a text block where the user can type in the name (or a portion
of the name) of an entry to search for; two radio buttons which enable
searching either for the name of a spectrum or the name of a molecule; and a
listing of all of the entries in the database.
It is important to note that the molecule name can include whatever
information regarding the sample that the user desires. For example, the molecule name can include
the experiment number, or the date on which the data was collected and
analyzed, etc. The spectrum name can
also be modified by selecting ‘Set Labels from the Edit Menu. The following dialog box will be displayed:
If
after creating the database the need to edit the database arises, the entries
can be edited by selecting Manage Custom Database from the File menu, or by
selecting Edit Custom Database from under the Edit menu (More details about
this can be found in the Edit -Custom Database section of this document). SpecMan allows the user to open multiple
spectra with one spectrum as an *.spd file and another as a non-*.spd
file. One application of this feature
is to manually search and compare the spectrum of an unknown with the known entries
in the database.
This
option is used for importing and displaying the *.mba files that are generated
by Spectrum Research’s 13C spectral prediction program,
NMR-SCAPE. By selecting ‘Import NMR-SCAPE
Database,’ the following dialog box will appear:
In
order to be able to view the *.mba file in SpecMan, the file needs to be
converted to a *.jdx file format, so enter a File Name and click ‘Save.’ To view the *.jdx file, select ‘Open
Spectrum’ from the File Menu.
This
option is used for saving the current list of displayed multiple spectra. This enables the user to save
a selected list of spectral data that can be accessed easily during a future
session for analysis. Upon selecting
this option, the following dialog box will appear:
Enter
the output file name, and the list will be save with the extension *.list. The next time that the user opens multiple
spectra, this file can be opened and all of the spectra listed in this file
will be displayed.
SpecMan can now prepare data for input into NMR-SAMS. The following options are available under
the pull-right menu of Prepare NMR-SAMS Data:
By
selecting Define Molecular Formula, the following dialog box will appear:
Select 'Browse' to
define the location for saving the NMR data and then type a filename (the
program will automatically add the *.nmr extension). Finally, input the molecular formula of the sample, or leave it
as “Unknown” if the exact formula is not known.
The
next step in preparing the NMR-SAMS data, is to convert the H-1 Peaks List into
the proper format for incorporation into NMR-SAMS. The following dialog box will appear when 'H-1' is selected from
the pull-right menu:
Select
the location of the H-1 peaks table, and the peak list will be converted and
written into the *.nmr file. A *.mdf
file is also created which contains the empirical formula information. In a similar manner, the peak lists for C-13
and DEPT; COSY; HMQC (or HETCOR); HMBC (or COLOC); NOESY (or ROESY); and
INADEQUATE can be converted (for more details, refer to the Q2 or Taxol
Tutorials). This function originally
resided only in NMR-SAMS, but is now also found in SpecMan. If a problem or error arises during data
conversion, it is now possible to compare the converted data with the original
spectrum and peak list information right in the SpecMan program. If the need to edit the converted data
arises, select NMR-SAMS data from the Edit Menu. More details regarding the editing of NMR-SAMS data can be found
in the Edit Menu portion of this document.
SpecMan can export spectra as Postscript (*.psf), GIF (*.gif), or
Acrobat (*.pdf) files. Select ‘Export’
and the following dialog box will appear:
It is important to note that only the spectra in the active spectrum
window will be exported. You will need
to make other spectral windows active before you can export their contents.
SpecMan now has the ability to print spectra, structures, peak tables
and assignment tables. The following
options are available from the pull-right menu of Print:
The active spectrum, the spectral windows (1D, 2D), the active
molecule, the molecule window, the peaks tables (1D, 2D, 3D), and the
assignment table can all be sent directly to the printer.
This
option is used for saving the current 2D spectral view as a new spectral data set. This enables the user to save selected spectral regions. Prior to selecting this option a zoom may be
performed. When 'Save Submatrix' is
selected, the following ‘Save As’ dialog box appears:
Type
a filename to define the folder name in which the submatrix will be saved with
appropriate parameter files. Click
'Save' to save the current expanded view as new spectral data. To save the transposed view of the spectrum,
select ‘Transpose Spectrum’ from the File Type option and then click 'Save'.
This
option is used for saving the 1D X or Y projection of 2D spectra. When this option is selected, the following
‘Save As’ dialog box appears:
This allows the user to save
either the X or Y projection. Once a
filename has been defined and the 'Save' button has been clicked, a folder with
the filename will be created and the projection will be saved in this folder as
a new spectral data file. In addition,
a *.prj file will be created in the original 2D spectral data folder.
To
exit SpecMan, use the File/Quit menu option.
If there are peaks tables open, SpecMan will ask if the user wants to
save them before exiting.
Chapter 4
This
chapter helps the user navigate SpecMan’s Edit Menu and its features, as well
as relevant main concepts and principles.
The Edit menu lists options related to the editing of spectral data into
and out of SpecMan. The Edit menu also
contains enhanced clipboard functions for report generation.
This option allows the user to reverse a previous
action. After performing an action that
the user wants to reverse, select ‘Undo’ from the ‘Edit’ menu, and the action
will be undone. Select the 'Redo'
option to re-perform the action that was just reversed and things will return
back to the previous display/action.
The following are a sampling of the actions that can be undone:
·
Manual
Peak Addition (All Options)
·
Merge
Peaks
·
Move
Peaks
·
Remove
Peaks
Hint: The text of the ‘Undo’
option changes to reflect the current action that can be undone.
Warning: Only the most recent action will be undone, so if an
action is perform after the error, SpecMan will not be able to undo the error.
Select
Copy Spectrum from the Edit menu to copy the spectrum in the SpecMan window and
the following pull-right menu will appear:
The
user can choose to copy just the active spectrum (if multiple spectra are
open), or the entire contents of the 1D spectral window or the 2D spectral
window by selecting from the three pull-right options.
Once
the spectrum/spectral windows have been copied, open up a Word document side by
side with SpecMan. Select Paste from
the Edit menu in the Word document to paste the spectrum into the Word document
as shown below:
Choose
Copy Molecule from the Edit menu to copy the molecule in the SpecMan
window. The following pull-right
options are available:
The
user can choose to copy the active molecule (if multiple molecules are open),
or the entire contents of the Molecule Window by selecting from the two
pull-right options.
Once
the molecule/molecule window has been copied, select Paste from the Edit menu
in Word to paste the molecule into the Word document.
Select
Copy Assignment from the Edit menu to copy the assignment table in the SpecMan
window. Then, open a Word document side
by side with SpecMan. Select Paste from
the Edit menu in Word to paste the assignment table into the Word
document. The assignment table will
appear in text format in the Word document.
In order to convert the assignment table into actual table format,
highlight the text portion of the assignment table, and under Word’s Table
menu, select Convert Text to Table and the following will appear:
Select
Copy Peaks from the Edit menu to copy the peaks table in the SpecMan
window. The following pull-right
options are available:
The
user can choose to copy the 1D, 2D or 3D Peaks Tables. Once a Peaks Table has been copied, select
Paste from the Edit menu in Word to paste the table into the Word document.
The
peaks table will appear in text format in the Word document. In order to convert the peaks table into
actual table format, highlight the text portion of the assignment table, and
under Word’s Table menu, select Convert Text to Table and the following will
appear:
SpecMan allows the user to
customize many of the display attributes to meet each individual's display and
interaction needs. Among these are
window sizes, fonts and colors, default values for parameters in the threshold
palette, and other attributes related to cursors and tables. This information is stored in the
specman.ini and specmanpersonal.ini files which should always remain in the
SpecMan directory. These files are
plain English text files and can be edited with any text editor. SpecMan reads the specman.ini file when the
user first initiates the program.
SpecMan allows the user to
customize its display by editing the specmanpersonal.ini file. To do so, select ‘Initialization File - Edit
Personal Ini’ from the Edit Menu. This
will bring up the following:
The
details of the specmanpersonal.ini file format are: Lines that begin with a pound sign (#) are
comments which are ignored by the program.
The other lines are of the format: <keyword> <value(s)>,
where <keyword> tells SpecMan what default is being set, and
<value(s)> is one or more numbers or letters that the default is being
set to. The actual number and type of
values are determined by the individual defaults. For example, the MainWindow keyword sets the location of the Main
SpecMan window on startup. It requires
2 integers specifying the x and y locations of the window. Therefore, its line looks like: 'MainWindow 20 50', which puts the Main
Window's upper left corner at the screen coordinate (20, 50).
The user can also choose
to toggle between the black default ini and the white default ini files. These are files supplied with SpecMan that
contain different color selections for backgrounds (a white background that is
useful when copying and pasting spectra, molecules, etc., and a black
background).
The % Version is for our internal usage, so do not alter
this line or the line below it, while the % Num lists the number of total entries
in the custom database. Lines beginning
with % cannot be edited, while the rest of the lines can be modified.
This feature
allows a NMR-SAMS Data file (*.nmr file) to be displayed in a text editor for
editing, as shown below:
SpecMan allows the user to change the spectral
labels and title. To do so, select ‘Set
Labels’ from the Edit menu and the following dialog box will appear:
Enter the desired new labels and then click ‘OK’ to
initiate the change. Note that this
will only affect the active spectrum (if multiple spectra are open). To change the labels of other spectra, first
set each spectrum as active and then select Set Labels.
When SpecMan imports processed spectrum files, it
reads the data's spectral parameters, such as spectrometer frequency, data
size, sweep width, etc. Although these
parameters are obtained from the original data, the user can modify them by
selecting ‘Spectral Parameters’ from the Edit menu.' The following dialog box will appear with the current spectral
parameters listed (for example, for a 1D spectrum):
Depending on the dimensionality of the experiment,
the dialog box will show parameters that correspond to different spectral
dimensions. For example, the parameters
for 1D spectra will have only the X dimension values, while the parameters
for 2D spectra will have values for the X and Y dimensions. The following spectral parameters dialog box
will be displayed for a 2D spectrum:
Dialog boxes associated with other types of spectral
data (MassSpec and UV, respectively) are also shown below:
After changing the spectral parameters, click 'OK',
and the new parameters will be saved in the data file for future use.
A spectral reference is a peak corresponding to a
known reference from which other frequencies are measured. When ‘Set Reference’ is selected from the
Edit menu, SpecMan displays a crosshair cursor and prompts the user to click on
a peak that can be used for setting the reference. Upon clicking on a 1D reference peak, the following dialog box
appears:
Next, enter the new reference points and reference
values. Depending on the dimensionality
of the data, the user will need to enter various reference points and reference
values. For example, 1D spectra only require the X coordinate, while 2D spectra require X and Y point coordinates and values, and 3D spectra
require X, Y and Z point coordinates and values, as shown below:
2D:
3D:
Dialog boxes associated with
other types of spectral data (MassSpec and UV, respectively) are also shown
below:
Click 'OK' to apply the new reference, and SpecMan
will store the new reference values in the spectral data file and update the
display with the new scales corresponding to the new reference frequency.
How to Set Reference on a 1D peak with respect to another reference peak in a related 1D spectrum:
This option enables the user to set reference on a
peak graphically without having to enter reference values. For example, this method can be used for
setting reference on a DEPT spectrum with respect to peaks picked in a 13C
spectrum. To do this, zoom in on a peak
in the DEPT spectrum to set reference on, and then load a 13C peaks
table with which you wish to match the reference. Next, select ‘Set Reference’
from the Edit menu, and place the cursor on the DEPT peak to align with the
peak label of the 13C peak.
Click the left mouse button and keeping it pressed (a symbol consisting
of a circle surrounding a ‘+’ sign will appear), drag the symbol until the
symbol lines up with the 13C peak label. Release the button and the set reference dialog box will
appear.
Internally, SpecMan computes the reference values
with respect to the peak label, and updates the corresponding X values in the
dialog box. Click ‘OK’ to accept the
new reference, and the spectrum scales will be updated with the new
values. In this manner the user can
align the 1D DEPT with the 1D 13C spectrum to maintain same spectral reference.
How to Set Reference on a 2D peak with respect to a grid line intersection based on 1D reference peaks:
This option enables the user to set reference on a 2D peak graphically without having to enter
reference values. To do this, the user
needs to zoom in on the peak and the grid line intersection to match. Next, select ‘Set Reference’ from the Edit
menu, and place the cursor on the center of the 2D peak to align. Click the left mouse button and keeping it pressed, drag the
symbol (a circle with a ‘+’ inside it) until the symbol lines up with the grid
line intersection. Release the button
and the set reference dialog box will appear.
Internally, SpecMan computes the reference values with
respect to the grid line, and updates the corresponding X and Y values in the
dialog box. Click’ OK’ to accept the
new reference, and the spectrum scales will be updated with the new
values. In this manner the user can
align 1D reference spectrum with a 2D spectra.
The
user can edit an active molecule by selecting ‘Molecule’ from the Edit
menu. This will bring up the following
Molecular Editor palette:
After
the Molecular Editor is displayed, the user may need to click ‘Clear’ to remove
the current displayed structure, or the user can build a structure starting
with the current displayed structure.
To sketch the target structure, first select Add, Atom, and Continuous
Mode. Leave Element as “C”, and
Ambiguous unchecked (this toggle is reserved for defining a substructure, and
is currently not used). Then click in
the main graphics window at the position where the first atom is supposed to
appear. An atom will be drawn at that
location and when the next location is clicked, another atom will be drawn with
a bond connected to the previous atom.
In this manner atoms are added at the locations where the user clicks
and bonds are added automatically between the current and last atom. To discontinue the addition of an automatic
bond between atoms, turn off the Continuous Mode.
Once
the skeleton has been sketched, the user can modify the structure. To modify an atom, select Modify and Atom,
and then type the desired element symbol after Element. The user can also move the slider to change
the valence of the atom (i.e., choose a valence different than the
default). Then click on the atom to change. To modify a bond, select Modify and Bond,
and then select the desired bond type. If the user is not sure about the
connectivity or attached protons of an atom, select Ambiguous. Next, click on the two associated atoms of
the bond to modify, and the bond will be modified. If Continuous Mode is on, use the middle (or right) mouse button
to pause the continuous mode temporarily.
To
delete an atom, select Delete and Atom, and then click on the atom to
delete. To delete a bond, select Delete
and Bond, and then click on the two associated atoms of the bond to
delete. After building the target
structure, click OK to accept it.
To
renumber an atom, select Renumber from the Molecular Editor dialog box. This feature will enable the user to
renumber atoms in a structure to conform to IUPAC or other conventions. Open a molecule along with its corresponding
assignment table, as shown below:
Next,
select Renumber in the Molecular Editor dialog box, and the dialog box will
appear as shown below:
Select
the number to begin renumbering with (for example, 1), and type it in the text
box next to Renumber. Then, click on
the first atom in the molecule (for example, atom 26) to renumber as atom 1. Internally, atom 26 will now become atom 1,
and the old atom 1 will be renumbered as atom 26. Additionally, the assignments will also be swapped so that they
remain with the correct atom, and the assignment table will be updated with the
new atom numbers. When another atom is
clicked on, the program will increment the initial renumbering number. For example, the next atoms will be labeled
two, three and so on. If the user had
begun renumbering with 20, then the next atoms would be labeled 21, 22, 23,
etc. The renumbering of atom 26 is
shown in the following window:
Comparison
of the initial molecule (shown on Page 41) with the above modified molecule
shows the old atom number 26 now renumbered as atom 1.
Chapter 5
The
Display menu lists options related to the graphical display of SpecMan. This chapter helps the user navigate
SpecMan’s Display Menu and its features, as well as relevant main concepts and
principles.
When multiple spectra are open, SpecMan allows the user to set one spectrum as active (referred to as
an active viewport) and all functions will be applied to the active
spectrum. To set a spectrum active,
select ‘Set Active Viewport’ form the Display menu and click on the desired
spectrum, and it will become active.
The color of the axes will be changed to reflect that the spectrum is
now active (Please note that the color of the axes is controlled by the
specmanpersonal.ini file’s ‘FrameColor’ and ‘InactiveColor’ options).
Please note that there are several menu items that
do not require user input, such as the zoom options, that can be applied to any
open spectrum. To use such functions,
simply click in the desired viewport.
By default, the order of displayed viewports is the
order that the 2D spectra were opened in.
To change this without reopening the spectra, select ‘Swap Viewports’
from the Display menu, and then click on the two viewports that you wish to
swap. The two viewports will then be
redrawn with the reordering of the 2 viewports. In this manner, any viewport order can be achieved through
subsequent selection of ‘Swap Viewports.’
The
Threshold palette is used for controlling the noise threshold used in the
generation of contours for the spectral display. The ‘Threshold’ option from the Display menu acts as a toggle
that displays and hides the threshold palette, as shown below:
The
controls in this palette can be used to control the following:
·
Adjust
the noise threshold for contouring by specifying a value or by dragging the slider bar.
·
Adjust
the contour level separation. This specifies the factor by which the base
threshold is multiplied to determine the cutoff of each contour level.
·
Adjust
the maximum number of contour levels to be drawn. The maximum levels allowed are 100. (If the cutoff of a level
exceeds the maximum intensity of the data points, then the maximum number of
levels is automatically set to the level that corresponds to the previous
cutoff).
·
Define
the starting level for display. This
feature allows stepping through the available contour levels. Performing this activity can assist in
resolving partially overlapped peaks and also locating peak tops.
·
Define
the type of contour levels (whether positive, negative or both) to be drawn.
The Reset button returns the palette values to the
defaults.
If
Auto Redraw is checked, then any change to the palette will be reflected
immediately. Otherwise, contouring will
only take place when the update button is checked. All operations described above will only be applicable to the
active spectrum. If the user wishes to
change the display attributes of another spectrum in multiple view mode, first
set the interested spectrum as active.
In the case of a 3D spectrum, select the ‘Apply
to all Tiers’ option in the Tier Palette to regenerate contours for all tiers
with the same threshold. When multiple
spectra are displayed, the Threshold palette is associated only with the active
spectrum.
By default, when displaying multiple 2D spectra,
viewports are displayed in a row-based square.
The following options are available from the ‘2D Viewport Layout’
pullright menu:
Row-based square
One row
Column-based square
One column
Depending on the type of spectra that the user is
working with, the user can change this to be one row, one column, or a
column-based square. To do this, select
the desired layout from the ‘Viewport Layout’ menu option on the ‘Display’
menu. The layout will be immediately
changed to the selected layout. The
user can also change the default selection by modifying the ‘ViewportLayout’
entry in the specmanpersonal.ini file.
Note that 1D viewports are always displayed in one column, regardless of the
setting of the viewport layout.
This feature allows the user to select the units for the X
and Y axes. By selecting ‘Units’ from
the Display menu, the following putllright menu will appear:
Select PPM, Data Points or Hertz to display the desired
units.
When working with multiple spectra of the same molecule, it can be convenient to tie the axes
display. This can be accomplished by
selecting ‘Tie Views’ from the ‘Display’ menu.
When this option is chosen, the following Tie Manager dialog box will be
displayed:
The
Tie All 1D option ties the X axes of all open 1D spectra. The Tie All 2D option ties the X axes and Y axes of all open 2D and higher spectra. The Untie All option removes all tying from all
open spectra. To tie the axes of two
specific spectra, select the First Spectrum and Second Spectrum text boxes to
specify the desired spectra to tie.
Then, click on either X&X to tie both of the X axes, or select
Y&X to tie one of each axis. Note
that in the tied mode the cross-hair cursors of each spectrum are also tied
together so that they move together when the user is scrolling in either
spectrum. Then, select OK and the
spectra will be tied as in the following:
In
the above view, the 13C spectrum is tied to the DEPT-135
spectrum. This enables the user to
align common peaks between the different 1D spectra and identify the
multiplicities in the Carbon data. Also
this can be used for setting the common spectral reference between Carbon and
DEPT data. The user can also perform 1D
peak picking and overlay the picked peaks on any related spectrum for
comparison in this multiple spectral view.
In
a similar manner, one can also use this feature for analysis of multiple 2D
spectra with tied frequency axes.
When working with multiple 2D spectra the following
Tie Manager dialog box will appear:
Click ‘OK’ and any 2D experiments (such as HMBC and
HMQC) will have tied axes as shown below:
When working with multiple 3D or 4D spectra (as in
SpecManPlus), the following Tie Manager dialog box will appear:
When comparing two similar peaks, it can be
beneficial to the user to have the option of overlaying the two spectra for
closer comparison. When selecting
‘Overlay’ from the Display menu, the user can choose to overlay with an offset
(adds an overlay ppm value to the overlaid spectrum which can be useful when
the ppm regions of the peaks don’t match exactly), or without an offset
(overlays according to the spectral ppm regions, with no offset added).
To overlay with a ppm offset, select ‘Overlay -
Overlay with Offset’ from the Display menu and then click on a spectrum to
overlay on the Active Spectrum. A
dialog box will appear that prompts the user to enter ppm offsets for the X and
Y dimensions. Entering zero (0) for a
dimension results in no overlay for that dimension. Click ‘OK’ and the overlaid spectrum’s viewport will disappear
and the spectrum will be drawn in the active Viewport (with the ppm values of
the overlaid spectrum shifted by the specified offset). The zoom features will now zoom both spectra
at the same time. Reselection of
‘Overlay - Overlay with Offset’ will remove the overlay.
To overlay without an offset, select ‘Overlay -
Overlay without Offset’ and then click on a spectrum to overlay on the Active
Spectrum. The overlaid spectrum’s
viewport will disappear, and the spectra will be drawn in the active Viewport. The following shows the original HMBC and
HMQC spectra and then the overlay of the HMQC spectrum (red) on the HMBC
spectrum (black):
Reselection of ‘Overlay - Overlay without Offset’
will remove the overlay.
Note: The overlaid spectrum is
displayed in a different color (red).
The default spectral colors are controlled by the ‘ExpPosColor’ and
‘ExpNegColor’ initialization file options.
The spectral colors of overlaid spectra are controlled by the
‘SecondPosColor’ and ‘SecondNegColor’ initialization file options.
SpecMan enables the user to display 1D reference spectra and their peak lists on a 2D spectrum for quick identification of missing and overlapping peaks,
and it is also used in grid-intelligence based peak picking. By selecting ‘ Associate 1D
Reference Spectra’ from the Display menu, the following will appear:
To associate a reference spectrum (displayed along
the axes of the 2D spectrum), check the box next to ‘1D Reference Spectral
Along X Axis’ and next to ‘1D Reference Spectral Along Y Axis’ and then select
the appropriate 1D spectral files. To
display each spectrum’s peak list (displayed as grid lines on the 2D spectrum),
check the box next to ‘1D Reference peak List along X Axis’ and ‘1D Reference
peak List along Y Axis’ and then select the appropriate 1D peak files.
Click ‘OK’ and the following will be displayed:
The association of reference spectra also aids in
the peak picking process by identifying the location of potential 2D peaks at
the intersection of the 1D peak lists’ gridlines (drawn parallel to X and Y
axis). SpecMan uses a novel
gridline-based auto peak picking algorithm to efficiently pick peaks in 2D spectral data. This algorithm
is particularly useful for peak picking the center of mass of crosspeak multiplets (for example, in 2D COSY, HMBC, etc.). The details
of using gridline-based peak picking are located in the ‘Analysis – Pick Peaks
Automatically – 2D’ section of this user guide.
The user also has to ability to associate a
Projection, Row, and/or Column of the current 2D spectrum. To associate a
Projection, check the box next to ‘2D Projection along X axis’ or next to ‘2D Projection along Y axis.’ Click ‘OK’ and the projection of the 2D spectrum will be displayed. To
view a particular row or column, check the box next to ‘Row’ or ‘Column’ and
enter the desired row/column numbers in the text box.
Please note that information regarding associated 1D reference spectra and peak lists, along with other attributes are
saved in an environment file (*.env) in the same directory in which the
original spectrum is located.
Therefore, the next time the spectrum is opened, the environment file
will be read and the 2D spectrum will be displayed along with the 1D reference spectra, lines, projections, etc.
Adjusting the vertical
scales of reference 1D spectra
Once the reference spectra have been displayed along
the X and Y axes, the vertical scaling of the 1D reference peaks can be adjusted by moving the arrow or crosshair
cursor to an intensity level (with respect to some strong 1D peak) on the 1D spectrum along the X axis (or Y axis), and click at the desired
level. All of the 1D peaks will be
enlarged vertically since the vertical scales have been changed. To reset the scaling to the original
display, move the cursor to a point below the base line of the 1D spectra and click the left mouse button. In a similar way, the 1D reference along the Y axis can also be re-scaled.
SpecMan
also allows the user to modify the maximum intensity of the Associated 1D Reference Spectra (useful if the 1D spectrum is of low concentration and the solvent peaks are much more
intense than the peaks of interest).
To
set the intensity cutoff, click on a point that will then become the new
maximum, and the 1D spectrum will be redrawn. The
user may reset the cutoff back to the highest point by clicking above the 1D drawing area, or between the 1D drawing area and the 2D axes boundary.
All 1D spectra are displayed in a window entitled, ‘1D Slices.’ The user can display or hide the 1D slice
window by selecting and de-selecting ‘1D Slice’ from the Display menu.
When the 1D slice window is displayed, a ‘1D Control
Panel’ will also appear, as shown below:
Prior to auto or manual 1D peak picking, the appropriate threshold level can be set by selecting ‘Set
Threshold’ from the 1D Control Panel. Next, place the cursor in the
1D slice window, and a red, horizontal line will appear. Move the red, horizontal line to an
appropriate level for the cutoff threshold for 1D peak picking and click the
left mouse button. The corresponding
threshold value will be updated in the 1D Control Panel, and this value will be used for peak picking. When the 1D automatic peak picking option is selected, this threshold value will
appear in the peak picking dialog box as the default threshold.
The 1D slice window is also used to display 1D
traces from a 2D or 3D spectrum. When a
2D spectrum is displayed in the main window and ‘Display – 1D Slice’ is
selected, the user can click on a cross peak with the crosshair cursor, and the
1D traces of rows and columns corresponding to this location will be displayed
in the 1D slice window, as shown below:
Similarly, when working with a 3D spectrum, all
three 1D traces (rows, columns and tiers) can be displayed by clicking the
crosshair cursor on a cross peak in a 2D tier plane of a 3D data.
When the 1D slice window is displaying 1D traces
from a 2D or 3D spectrum, the following ‘1D Control Panel’ will appear:
This
feature allows the user to display different features of a molecule. When Molecule is selected under the Display
menu, the following pull-right options are available:
Window - This
will allow the user to close or display the molecule window.
Chemical Shifts - This
will allow the user to display chemical shifts related to the molecule.
Carbon Symbols - This
will allow the user to display the atoms with their Carbon symbol.
Atom Numbers - This
will allow the user to display the atom numbers.
Balls - This
will allow the user to view the molecule with the atoms as balls.
Protons - This
will allow for the protons to be visible.
Molecular Formula - This
will allow the molecular formula to be visible.
Molecular Weight - This
will allow the molecular weight to be visible.
Refine - This
option allows the user to refine the display of the molecule.
This option allows the user to display or hide the
1D and 2D Peaks Tables that are associated with spectral data by selecting and
reselecting ‘Peaks Table – 1D/2D’ from the Display menu. A 1D Peaks Table is displayed below:
The details for each row in the 1D peaks table are listed below:
|
Column Name
|
Description
|
|
ID
|
This represents a unique number that SpecMan uses
for book keeping
|
|
Label
|
This represents the label assigned to a peak by
the user. This label is used for
annotating the peak in the spectral view.
|
|
X Point
|
This represents the Data point location of the
peak along the X axis. It corresponds to the actual data point in the
spectrum.
|
|
X Value
|
This represents the frequency/chemical shift value
in the appropriate units for the X data point in the spectrum. These numbers are based on the spectral
reference that has been used.
|
|
Multiplicity
|
Multiplicity of the peak. Currently, all peaks have the Multiplicity
of u (unknown). This column is
reserved for future expansion.
|
|
Intensity
|
This represents the intensity of the peak. These intensities can also be used for NOE
distance calibration of NMR spectra.
|
|
File
|
This represents the Spectral Data File that
generated the list of 1D picked peaks. For peaks
that have been picked on 1D rows or columns the word Row or Column is printed
in this column
|
A 2D Peaks Table is
displayed below:
Each entry in the table represents a single
peak. The details of the columns in
each row of the 2D table are given below:
|
Column Name
|
Description
|
|
ID
|
This represents a unique number that SpecMan uses
for book keeping
|
|
Label
|
This represents the label assigned to a peak by
the user. This label is used for
annotating the peak in the spectral view.
|
|
X Point
|
This represents the Data point location of the
peak along the X axis. It corresponds to the actual data point in the
spectrum.
|
|
Y Point
|
This represents the Data point location of the
peak along the Y axis . It corresponds to the actual data point in the
spectrum.
|
|
X Value
|
This represents the frequency/chemical shift value
in the appropriate units for the X data point in the spectrum. These numbers are based on the spectral
reference that has been used.
|
|
Y Value
|
This represents the frequency/chemical shift value
in the appropriate units for the Y data point in the spectrum. These numbers are based on the spectral
reference that has been used.
|
|
J Coupling
|
J coupling constant for this peak. Currently, all peaks have the J Coupling
value of 0. This column is reserved
for future expansion.
|
|
Multiplicity
|
Multiplicity of the peak. Currently, all peaks have the Multiplicity
of u (unknown). This column is
reserved for future expansion.
|
|
Intensity
|
This represents the intensity of the peak. These intensities can also be used for NOE
distance calibration of NMR spectra.
|
|
File
|
This represents the Spectral Data File which
generated the list of 2D picked peaks. For peaks that have been picked on
1D rows or columns the word Row or Column is printed
in this column.
|
A 3D Peaks Table (available
in SpecMan+) is displayed below:
Each entry in the table represents a single
peak. The details of the columns in
each row of the 3D table are given below:
|
Column Name
|
Description
|
|
ID
|
This represents a unique number that SpecMan uses
for book keeping
|
|
Label
|
This represents the label assigned to a peak by
the user. This label is used for
annotating the peak in the spectral view.
|
|
X Point
|
This represents the Data point location of the
peak along the X axis. It corresponds
to the actual data point in the spectrum.
|
|
Y Point
|
This represents the Data point location of the
peak along the Y axis. It corresponds
to the actual data point in the spectrum.
|
|
Z Point
|
This represents the Data point location of the
peak along the Z axis. It corresponds
to the actual data point in the spectrum.
|
|
X Value
|
This represents the frequency/chemical shift value
in the appropriate units for the X data point in the spectrum. These numbers are based on the spectral
reference that has been used.
|
|
Y Value
|
This represents the frequency/chemical shift value
in the appropriate units for the Y data point in the spectrum. These numbers are based on the spectral
reference that has been used.
|
|
Z Value
|
This represents the frequency/chemical shift value
in the appropriate units for the Z data point in the spectrum. These numbers are based on the spectral
reference that has been used.
|
|
J Coupling
|
J coupling constant for this peak. Currently, all peaks have the J Coupling
value of 0. This column is reserved
for future expansion.
|
|
Multiplicity
|
Multiplicity of the peak. Currently, all peaks have the Multiplicity
of u (unknown). This column is
reserved for future expansion.
|
|
Intensity
|
This represents the intensity of the peak. These intensities can also be used for NOE
distance calibration of NMR spectra.
|
|
File
|
This represents the Spectral Data File that
generated the list of 3D picked peaks. For peaks that have been picked on
3D bricks from a 4D spectra, the brick PPM is printed in this column.
|
Edit Peaks Table
SpecMan allows the user to edit the peaks tables by
selecting ‘Edit Table’ from the 1D Peaks Table. The following ‘Edit Peaks Table’ dialog box will appear:
