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Menus |
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The Control Panel is the first window to be displayed when NMRView starts up, and consists of a single menubar. Note that on Mac OS X the menubar will generally be displayed not as a separate window, but on the Desktops screen menu bar. The menus available through the menubar may be used to bring up various other NMRView windows. The options available through each menu item are summarized below.
###File
Projects
:
New
: Create a new project. You will be presented with a file browser to use in specifying the location
and name of the new project. The project will be created as a new folder with appropriate sub-folders.
Open
: Open an existing project. You will be presented with a file browser to use in selecting the existing project.
Recent
: A menu displaying recently used projects (up to 20). Selecting a project name from the menu will open that project.
Save
: Save the current project (including STAR3 file and open windows).
Save...
: Save the current data as a new project. (including STAR3 file and open
windows).
History
: Display a list of saved states of the current project. Selecting an item from the list
and clicking Open will reload the project as contained in that saved state.
Attributes
: Display the project attributes browser used to manage NMRVIEW projects. Use the
attributes browser to set attributes like locations of dataset folders.
Close
: Close the current project. This removes all open information such as datasets, peak lists, and
molecular structures.
STAR
:
Read STAR3
: Brings up a file selection panel for reading a BMRB Star file
(NMRView database file). Almost any kind of analysis that
NMRView can perform can be stored in a Star file.
Save STAR3 As...
: Brings up a file selection panel for writing a BMRB Star File.
Save STAR3 (Auto Increment)
: Saves a BMRB STAR file using a name automatically generated from
the last saved STAR file. For example, if the last file saved
was "myproject\_3.str" the new file will be "myproject\_4.str".
This is a convenient way to make frequent updates of your data
to a STAR file as you work on a project. To have this work
properly you should start with an initial file name that ends
with a non-integer character followed by an integer value (as in
the above example).
Fetch From BMRB...
: Load the set of files found in your last session. Each time you
use Scan Directory (or Clear and Scan Directory) the files found
will be stored in a file. The files in this table will be
opened.
STAR2 (deprecated)
: Earlier versions (before 8.0) of NMRViewJ used the STAR 2 file
format. If you need to work with these older files use the
choices in this menu. But some features of NMRViewJ (especially
relating to RunAbout) can only be saved in STAR 3 files, so its
a good idea to switch to the newer format. You can open a file
in STAR 2 format, and save it out in STAR 3 format.
Read STAR2 File
: Use a File Browser to Open and read a STAR (version 2.x)
File
Write STAR2 File
: Use a File Browser to Save a STAR (version 2.x) File.
Preferences...
: Select Prefs to open up the Preferences Panel. This can be used to set various user preferences for NMRView. On Mac OS X this menu item will be found under the NMRVIEW menu
: Print the active spectrum.
Show Console
: Show the NMRView console. The console can be used for command line input and displays the output of various commands. The NMRView console is based on the tkCon console developed by J. Hobbs.
Quit
: Quit the NMRVIEW program.
###Datasets
Open Datasets
: Select this to open a File Selection Panel that can be used to select datasets to be opened.
Open and Draw Datasets
: Select this to open a File Selection Panel that can be used to select datasets to be opened. When the dataset is opened a window will be created and the dataset will be drawn
Datasets Table
: Select this to open a window containing a table of all currently opened datasets. The use of this table is described in the chapter on Datasets.
Load Recent Datasets
: When you quit from NMRViewJ the file paths for currently opened datasets are stored into a preferences area containing recently opened datasets. Selecting this menu item will load these recently opened datasets.
Convert Varian Phasefile
: Varian phase files are stored as serial files (see Datasets chapter) and thus are less efficiently accessed than NMRView format files. Select this menu entry to get a file selection dialog to select a Varian phase file that can then be converted into an NMRView format file. The phase file must exist in the normal Varian directory hierarchy so that the procpar file can be read as well.
Manage Datasets
: Select this to open a Datasets Manage Panel that can be used to reference or close datasets.
Make Pseudo3D
: Select this to combine a set of selected 2D datasets into a single 3D dataset where each 2D dataset is on a plane. Choosing this menu item will display a file browser you can use to select the datasets with. After selecting datasets you'll be prompted for the name of the 3D dataset to create.
Peak Pick All
: Select this to pick peaks in all currently opened datasets. As with the similar operation available from the Datasets table this is only useful if the datasets have reasonable default contour levels (or if a reasonable value can be automatically determined from the datasets signal to noise level).
###Windows
Copy
: Select this to copy an image of the current spectrum window to the clipboard from where it can be pasted into another application
Synchronize...
: Display an interface in which you can set up synchronization of the view between various specified spectral display windows.
Export...
: Export a graphics file rendering of the current spectrum. You will be prompted for the file name and type of graphics file. Current formats include vector formats such as EPS, PDF and SVG and bitmap formats such as GIF, JPEG and PNG
Attributes...
: Select this to open a File Selection Panel that can be used to select datasets to be opened. When the dataset is opened a window will be created and the dataset will be drawn.
Monitor Crosshair...
: Open a window that will display the current chemical shift positions of the two crosshairs in the active window. If the window is displaying a dataset with three or four dimensions then the chemical shift ranges of the displayed planes will also be displayed. The row labeled "D:" in the monitor window will display the chemical shift difference between the two crosshairs for the x and y dimensions, and the difference between the top and bottom displayed plans for z and z2.
Manage...
: Select this to open a Windows Management Panel that can be used to raise spectrum windows to the front of the display or to delete them.
Key Bindings...
: Display the graphical interface for displaying the bindings that relate key presses in a spectrum window to actions that occur.
Strips (Canvas)...
: Select this to open display a dialog from which you can create a series of strips of spectra, as documented in the "Strips" chapter.
Save Dataset Section
: Select this to save the area of the dataset between the crosshair cursors into a new smaller dataset. You'll be prompted with a file dialog to choose the file name and after saving asked if you want to open up the new smaller dataset.
Favorites...
: Display a list of currently saved spectral views (favorites). Only active if a project is open.
Jump Panel...
: Display a graphical interface used for jumping around to various positions in spectra.
Hide all Spectra
: Hide all windows with spectra.
Show all Spectra
: Show all windows with spectra.
###Canvas
In premium mode, spectra can be displayed in windows that can include not only spectra, but also a wide variety of graphical objects such as rectangles, text, and lines. Canvases can also include various charts, including xy and bar charts.
File
:
Save...
: Save a NMRViewJ/dataChord format canvas file. This will save all
the graphic items on a single canvas (which may include multiple
spectra).
Open...
: Open a NMRViewJ/dataChord format canvas file. This will create a
new toplevel window containing all the graphic items in the
saved file. Spectrum items in the graphic file may depend for
their display on the datasets used in originally drawing them.
The software will check if the dataset are already opened,
attempt to open them from locations specified in the graphics
file or in your current project directories. If they can't be
found you will be prompted with a file browser to explicitly
open them.
Browse...
: Display a browser to let you browse through saved canvas files.
Export (Bitmap Image)...
: Export a graphics file rendering of the current spectrum in a
bitmap format such as PNG, GIF, or JPG.. You will be prompted
for the file name. The file format will be determined from the
extension of the file name.
Export (Vector Graphics)...
: Export a graphics file rendering of the current spectrum. You
will be prompted for the file name and type of graphics file.
Current formats include vector formats such as EPS, PDF and SVG
and bitmap formats such as GIF, JPEG and PNG. This menu item
will let you select both vector formats and bitmap formats, but
it is preferable to use the previous menu item for bitmap formats.
New
:
New Spectrum
: Create a new toplevel canvas window with a spectrum item in it
and the spectrum control iconbar across the top.
New Spectra
: Create a new toplevel canvas window with a multiple spectra in
it and the spectrum control iconbar across the top. You will be
prompted for the total number of spectra and the number of rows
in the display grid.
New Figure
: Create a new toplevel canvas window without any content (or
iconbar).
Insert
:
Spectrum
: Insert a new spectrum item onto the canvas.
Rectangle
: Insert a new rectangle item onto the canvas.
Text
: Insert a simple text item onto the canvas. You can change the
font and color of simple text items, but don't have control over
individual characters or more complicated attributes.
Formatted Text
: Insert a new formatted text item onto the canvas. Formatted
items can have most any attributes (font, superscript, bold,
italics, etc.) changed and special symbols added.
Annotation
: Insert a new annotation item onto the canvas. Annotation items
are a line with a simple text string at one end and an arrow
head at the other.
Table
: Insert a new table item onto the canvas. Table items are text
formatted as a table.
Line
: Insert a new line item onto the canvas.
Arc
: Insert a new arc item onto the canvas.
Oval
: Insert a new oval item onto the canvas.
XY Plot
: Insert a new xy plot onto the canvas.
Bar Plot
: Insert a new bar plot onto the canvas.
Stat Plot
: Insert a new statistical bar plot item onto the canvas.
Edit
:
Cut
: Remove the currently selected item(s) from the canvas. Cut items
will placed on the clipboard so they can be pasted elsewhere.
Copy
: Copy the currently selected item(s) onto the clipboard.
Paste
: Paste items on the clipboard into the current canvas. Items can
be items that were cut or copied from a canvas, or various other
item types copied from other programs including text and images.
Arrange
:
Send to Back
: Send the currently selected item to be below all other canvas
items.
Send Backward
: Send the currently selected item to be below the next lowest (in
display order) item in the canvas.
Bring Forward
: Send the currently selected item to be above all other canvas
items.
Bring to Front
: Send the currently selected item to be in front of the next
highest (in display order) item in the canvas.
Group
: Group together currently selected items. Grouped items will be
moved together when they are dragged around the canvas with the
mouse.
UnGroup
: UnGroup the currently selected items.
Lock
: Lock the currently selected items. Locked items can't be moved
or resized. The selection handles of locked items will contain
an "x" symbol.
Unlock
: Unlock the currently selected items.
Arrange Spectra
:
Horizontal
: Distribute all spectra in the canvas so they are evenly
distributed in a row across the canvas.
Vertical
: Distribute all spectra in the canvas so they are evenly
distributed in a column down the canvas.
Grid
: Distribute all spectra in the canvas so they are displayed as a
grid with a number of rows and columns that can accommodate all
the spectra.
Minimize Borders
: Adjust the display of axes and border sizes for efficient use of
space in gridded windows. Only axes along the left and bottom
sides of the canvas will be shown. This is the default when
gridded windows are first created.
Normal Borders
: Adjust the display of axes and border sizes so that the left
vertical and bottom horizontal axes are shown for all windows.
Stripify
: Open and setup the strip control dialog for the current canvas
spectrum.
By Type
: Arrange all spectra so they are in a reasonable layout based on
type (for example, HSQC occupying most space, with proton across
top and carbon across side).
Graphical Inspector...
: Display the Graphical Inspector that can be used to view and change the attributes (colors, fonts, sizes etc.) of items on the canvas.
###Peaks
Show Peak Inspector...
: Select this to bring up Peak Analysis Panel that can be used to display and edit information about peaks, including their assignment value, chemical shift positions, widths and intensities.
Add Peak Inspector
: More than one peak inspector can be displayed. This will create a new one.
Show Peak Table...
: Whereas the Peak Analysis Panel displays information about one peak at a time the Peak Table displays a table of information about every peak in a selected peak list. The table can be sorted and groups of peaks marked for deletion.
Add Peak Table...
: More than one peak table can be displayed. This will create a new one.
Peak Lists Table
: Show a table of all the open peak lists. This will include a row for each peak list with the peak list name, the dataset (if any) assigned to that peak list, the number of peaks in the peak list, the number of deleted peaks, the number of peaks with full assignments, the number of peaks with partial assignments, and the number of unassigned peaks.
File
:
Write List
: Write the peak list displayed in the current peak inspector to a
text file (.xpk).
Write Aria XML List
: Write the peak list displayed in the current peak inspector to a
text file in the XML format used by ARIA.
Read List
: Read an NMRVIEW format (.xpk) file in.
Make New List
: Create a new empty peak list. You will be prompted for the names
for the dimensions the list will have. This command is for
various advanced uses.
Read All Lists
: Read all the peak list files (.xpk) in the current working
directory.
Write All Lists
: Write all the current peak lists to NMRVIEW format (.xpk) files.
Read Sparky Save File
: Read in a text file created with the Sparky save command. A new
peak list with the contents of the file will be created.
Edit
:
Compress
: Remove peaks that have been marked for deletion. This is not
reversible, and will create gaps in the peak numbering.
Degap
: Renumber peaks (after compressing the list) so that there are no
gaps in the peak numbering.
Compress and Degap
: Combination of compress, followed by degap. Peaks will be
permanently deleted, and the list will be sequentially numbered
with no gaps.
Delete List
: Delete the current list displayed in the peak inspector.
Reference
: Display a graphical interface for setting various attributes of
the current peak list.
Couple
: Display a graphical interface that can be used to collapse
multiple peaks separated by defined splittings into a single
centered peak.
Cluster
: Cluster peaks in the current list based on their chemical shifts
in certain dimensions. Dimensions used and the tolerance that
determines whether peaks are clustered are set with a peak
template. Peak dimensions that are clustered will have a common
resonance id after clustering.
Fit
: Not yet active.
Partners
: Search all lists for peaks whose chemical shifts (for matching
dimensions) are similar (within the id tolerance) of the shifts
of the current peak. Matching peaks are listed to console.
Identify
: Display the Peak Identification interface. This interface will
suggest possible assignments for the current peak based on the
chemical shifts of assigned atoms, and distances in the current
structures.
Filter
: Display the Peak Filtering interface. This interface allows you
to delete peaks based on various criteria.
Analyze
:
HNHA
: Display an interface for measuring HN-HA coupling constants as
described in Kuboniwa et al. J. Biomol. NMR 4 (1994), 871-878:
HetNOE Analysis
: Display an interface for measuring the heteroncuclear NOE using
peaks in the current list and two datasets, one with, and one
without, the NOE active.
Minimum Chemical Shift
: Display an interface for measuring the minimal chemical shift
change for each residue in a chemical shift perturbation
experiment (typically in the presence of a ligand).
Peak Peak Matching
: Display an interface for coming up with the optimal matching of
peaks in two different lists.
Atom Peak Matching
: Display an interface for coming up with the optimal matching of
peaks in one list with the chemical shift assignments of the
current molecule.
Check
:
Check Pattern
: Each peak list can have a set of patterns (like i.hn, i-1.c
etc.) for the types of atoms that give rise to the peaks. This
command displays an interface used to check the consistency of a
peak lists assignments with its patterns.
Check Assignments
: Check the assignments of a selected peak list with expected
values for the assigned atom types (based on BMRB statistics).
Search Peaks
: Display an interface used to search peak lists for peaks based
on various criteria.
Integrate
:
Associate Dataset
: Each peak list has an associated dataset. By default this
dataset is the one from which the list was originally picked.
You can use this command to select a dataset to be assigned to a
list.
Get Volumes
: For each peak in the list, integrate the intensities over the
"footprint" of the peak in the dataset associated with this
list.
Get eVolumes
: For each peak in the list, integrate the intensities over the
optimal elliptical "footprint" of the peak in the dataset
associated with this list.
Get Intensities
: For each peak in the list get the intensity at the peak center
from the dataset associated with this list.
Plot Vol. vs. Intensities
: Plot an XY chart with the one symbol for each peak positioned on
the X axis at the peaks intensity, and the Y axis at the peaks
volume.
Plot Intensities
: Sort the peaks by their intensities and plot the peak
intensities in decreasing order.
Plot Volumes
: Sort the peaks by their volumes and plot the peak volumes in
decreasing order.
###Assign
Atoms...
: Select this to bring up the Assignments Panel that is used to keep track of chemical shift assignments.
Resonances...
: Add a peak at the position of the black crosshair.
Sequence...
: Select this to bring up a sequence display panel to display the residue sequence of the molecule.
NOEs...
: Select this to bring up a panel for creating and editing NOE restraint lists.
Constraint Table...
: Display a table for identifying NOES, and generating and analyzing distance constraints.
Dihedral Table...
: Display a table for generating and analyzing angular constraints.
###Analysis
RunAbout
: Select this to open up the RunAbout tool used for assigning proteins using triple resonance NMR experiments.
Rate Analysis
: Select this to bring up a panel for analyzing time-dependent properties (e.g., relaxation).
Titration Analysis
: Select this to bring up a titration panel for analyzing titration data.
IPAP
: IPAP is a set of experiments and an analysis protocol for measuring dipolar coupling constants in partially oriented media.
###Molecule
Read/Write Topology
:
Sequence GUI
: Distribute all spectra in the canvas so they are evenly
distributed in a row across the canvas.
Sequence File
: Bring up a file selection dialog to select and open a file
containing an amino acid, DNA, or RNA sequence. See the section
on Molecular Structures to learn about the
format of this file.
PDB File (using library)
: Bring up a file selection dialog to select and open a PDB format
file. This is the standard way to read in pdb files. NMRView
first reads the pdb file to determine the amino acid sequence.
Next, it reads the corresponding residues from the residue
library. Finally, it reads coordinates from the pdb file for
those atoms that have names matching the names in the residue
library. Atoms, that do not have a match in the residue library
will not be entered into the structure list. Atoms that are in
the residue library but not in pdb file, will be included in
structure list but will not be displayed. See the section on
Molecular Structures to learn about using
molecular structures in NMRView.
PDB File
: Reads a file of atomic coordinates of a macromolecule. File must
be stored in the PDB format as defined by the Protein Data Bank
(now the RCSB). This command does not also read from the residue
library so no connectivity information is available. If this is
needed use the pdb command instead.
Ligand File (.mol, .sdf)
: Open a small molecule (.mol or .sd) file and add it to the
current molecular topology.
Write ARIA XML Molecule
: Write a text file representation of the current molecule in the
ARIA XML format.
Nomenclature
:
Check/Change Nomenclature...
: Analyze the names of the atoms in the current molecule to
determine if you are using the IUPAC or XPLOR style of
nomenclature. A selection of atoms violating the most-likely
nomenclature will be listed.
Renumber...
: Offset the residue numbering (and any assigned peaks) by a
specified number.
Read Coordinates
:
PDB File...
: Bring up a file selection dialog to select and open a PDB format
file. Reads the PDB file filename and attempts to match the
atoms to atoms in the structure in memory. If atoms match by
residue name, atom name, sequence number, chain id, and
alternate identifier then the coordinates corresponding to each
atom matched are assigned the value of the coordinates of that
atom in file.
PDB File (multiple files)...
: Reads in coordinates from a series of PDB files. All PDB files
in the directory are read that whose name ends in an integer
value (like file1.pdb, file03.pdb, file41.pdb etc.). Each
coordinate set is stored a separate structure identified by the
integer number in the file name. The command only reads in the
coordinates, the topology must have been read in previously.
PDB File (representative)...
: Reads in coordinates from a single file and stores it in
structure 0. Information about the structure is stored in the
STAR Saveframe for a representative structure.
SD File...
: Bring up a file selection dialog to select and open an SD format
file (commonly used for "small" molecules)
Analysis
:
Structures...
: Display an interface for selecting which structures will be used
in other tools like the peak identification and constraint
table, and for calculating superpositions and residue rms
values.
Viewer...
: Display a molecular viewer for visualizing the current structure
and constraints(Premium feature).
###Help
About...
: Display a window showing various details about the currently running instance of NMRVIEW
Manual...
: Display the full manual for NMRVIEW
Send Bug Report...
: Display an interface in which you can compose a bug report to be sent via your email program.