Manual

Overview

The GUI of HELIS consists of two main regions: the left control panel, which includes buttons and a list box for managing filament data, and the right panel, which displays the views of filaments.

There are two types of views: the tomogram view and the filament view. These can be switched by clicking the view tabs. The tomogram view displays the slices of the tomogram and the filament axes, allowing users to coarsely determine and check the filament positions.

The filament view focuses on a selected filament and contains three sub-views: the averaging cylindrical surface, the cross-section, and the unrolled Fourier spectrum. These sub-views collectively provide intuitive insights into the selected filament, enabling users to precisely tune filament axis positions and determine helical symmetry.

Load Data

Click the Tomo button to select and load a tomogram file.

• Only .mrc files are supported.
• This step is required for subsequent operations.

Click the Fila button to select and load a filament information file.

• This should be a .mat file generated by HELIS.
• If filament positions already exist, this step can be skipped.

After successfully loading the tomogram and filament information, the tomogram view will display slices of the loaded tomogram, and the filament list box will list the existing filaments.

Observe Tomograms and Filaments

• Use the up or down arrow buttons to change the displayed layer, or directly input the target layer number in the edit box.
• Click the Flip Contrast button to flip the tomogram contrast.
  • This affects only the display in the GUI and does not modify the original data.
• Click an item in the Filaments list box to select the corresponding filament.
• Click the Show button to display all filaments simultaneously.

Edit Filaments

Add Filaments

• Click the Add Filament button to enter filament-adding mode.
• Click on the tomogram layer to pick filament axis points in order.
• Use the Undo button to cancel the previous point selection.
• Click the Accept button to save the selected points as a new filament and exit filament-adding mode.
  • The new filament will appear in the Filaments list box.
• Click the Close button to discard the current selections and exit filament-adding mode.

Delete Filaments

• Select a filament in the Filaments list box, then click the Delete button to remove the selected filament.

Save Filaments

• Click the Save button to save all filaments to a specified file.

Tune Filaments

Enter and Exit Filament Tuning Mode

• Select a filament and click the Tune Filament button to enter filament-tuning mode.
  • Any subsequent operations will modify the selected filament.
• Click the Update button to save modifications and refresh the filament view.
• Click the Abort button to discard all changes since the last update.
• Click the Finish Tuning button to discard unsaved changes and exit tuning mode.

Observe the Filament View

• Click the Filament tab to switch to the filament view.
  • The Filament tab contains three sub-views: the unrolled surfaces, cross-sections, and the cylindrical Fourier spectrum.
• Clicking on the unrolled surfaces will display the corresponding cross-section.
  • You can also input a value in the Section Pos edit box to modify the section's position.
• Use the Avg Num edit box to control the number of sections to be averaged.
• Set the Inner Rad and Outer Rad values to define the filament's inner and outer radii. These radii will be represented as two rings in the filament section figure.

Select the Target Filament Point

• Use the Next Pt or Prev Pt buttons to navigate between points.
  • The tomogram view and filament view are synchronized; selecting points in one view will affect both.

Edit Filament Points

• Add Points:

  • Click the Add Pt button to enter point-adding mode. Select a point by clicking on the tomogram layer or cross-section.
  • The new point will be added to the nearest end or inserted between two closest points.
  • After adding a point, the GUI will automatically exit point-adding mode. To add another point, click Add Pt again.

• Move Points:

  • Select a point and click the Mov Pt button to enter point-moving mode. Move the point by clicking on the tomogram layer or cross-section.
  • The GUI will automatically exit point-moving mode after the operation.

• Remove Points:

  • Select a point and click the Rmv Pt button to delete it.

• Cancel Operations:

  • If you mistakenly enter point-adding or point-moving mode, click the Cancel button to exit.

Note: Always click Update after making changes to refresh the filament view.

Automatically Trace and Center Filaments

• Set a threshold in the Thres edit box for tracing.
• Click the Trace button to trace the filament being tuned.
  • Use the tomogram layers to verify the results.
• Click the Centering button to automatically find the center of the filament.
  • This operation uses the extracted filament density map, ignoring newly added points. Ensure you have updated the filament before auto-centering.

Determine the Helical Parameters

Adjust the Shown Fourier Spectrum

• Click the Rmv Bg button to remove the background from the spectrum.
• Use Gamma to adjust the logarithm constant (details are shown in the GUI).
• Set Seg Size and Seg Step to define the segment length and step size for spectrum averaging.
• Max Ord adjusts the horizontal width.
• Use Δn and ΔL to define the search range for vector optimization.
• a* and b* are the reciprocal primitive vectors, while the star number, rise, and twist represent the corresponding helical parameters. These are read-only values.

Determine Reciprocal Primitive Vectors and Helical Parameters

• Click the Set Va or Set Vb button to manually set the 1st or 2nd reciprocal primitive vectors (RPVs) by selecting points on the Fourier spectrum.
• Click Opt Vs to optimize the manually specified vectors.

Averaging

• Click the Avg Surf button to average the unrolled surface.
• Click the SF-STA button to reconstruct the SF-STA of the tuned filament.