The menu
bar is organized into Project, Data, Particle,
Function, Parameter
and Help
pull-down menus.
Project Menu
New :
Create a project space to host all data files for a molecular system
being studied. When prompted, define a
location for the new project space from the pop-up window. The
extension ".ems" will be automatically attached to the specified name,
after which a
directory will be created (i.e., "project_name.ems"). The
project name
will appear at the upper right corner of the GUI window. Under the
project space directory, there will also be several sub-directories:
- micrograph : to
store micrographs, screening masks and pre-processed image data
- template
: to store template images and masks (both L1 and L2 masking)
- screening
: to store parameters and scores for automated particle
screening
- particles
: to store particle selections (coordinates and/or
frames)
- alignment
: to store aligned particle frames and classification result
- frealign
: to store parameter files for FREALIGN model refinement
- modeling
: to store data for density modeling and analysis
Inside the project space, files are named after the respective
micrograph images, with variations in the extension. For example, given
a micrograph image "1234.mrc",
the corresponding particle selection (Signature
format) would be named "project_name.ems/particle/1234.ptk".
Since the
project space
is internally managed by Signature,
the user should not tamper with
either the files or the directory structure.
Open : Load an existing
screening/lignment project definition.
Save : Save a newly
established screening/alignment project definition.
Close : Close a project and
reset the system.
Exit : Terminate the
program. If necessary, the system will prompt to save the current
project.
Data Menu
Micrograph
: Open a 2D micrograph image (in MRC or SPD format).
Template
:
Open an MRC template stack. "Inclusive" and "Exclusive" functions set
Inc/Exc flag for all templates.
Density
Map : Switch to 3D
Model
OpPanel and load an MRC density map.
Particle Menu
Clear
Selection
: Clear the current particle selection. All categories of
particle selection - automated selection (red marker), manual selection
(blue marker) and confirmed selection (green marker) - will be removed.
Clear
Alignment
: Clear the alignment parameters of particles in Image
Stack Editor.
Load
Particle Coordinates : Open an existing particle coordinates
file. In addition to the proprietary PTK format, the system also
supports the IMAGIC and SPIDER formats.
Save
Particle Coordinates : Store the current particle coordinates
to a file. In addition to the
proprietary PTK format, the system also supports the IMAGIC and SPIDER
formats.
Save
Image Frames : Store the current particle selection as images
to a 3D MRC stack. The size of each image frame is equivalent to that
of the template images.
Export
Frealign PAR : output particle alignment parameters to a
Frealign PAR file.
Function Menu
Image
Stack Editor : Launch an MRC image stack browser, which also
provides frame editing and image processing functions.
Digital
Gel Filtration : Visualize the density-mass distribution of the
particles inside Image
Stack Editor.
Particle
Alignment : Align and classify the particles inside Image
Stack Editor.
Parameter Menu
Load :
Set the input parameters on the GUI to customized values.
Save
: Store the customized parameters on the GUI to a file.
Default
: Reset the parameters on the GUI to the system default values.
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