Menu Bar (Menu)


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.