User Manual

  1. Select the "Submit job" option in the home page and this will re-direct to the submit page.
  2. Option is provided to give either the EMDB Id or upload the file in vtk format.The EMDB Id should have only numbers in it. For example: If the symmetry in EMDB dataset 1134 has to be checked, the user can just type 1134 in the box given.
  3. Max/Min: This is an option to determine the symmetry with respect to maximum or the minimum region of the contour. Its value is by default minimum.
  4. The values of Approximation parameter, Stabilization parameter and noise threshold should be between 0 and 1.
    1. Approximation Parameter: Specifies when two contour surfaces may be considered similar to each other.
    2. Stabilization parameter: Specifies the size of the neighbourhood of a saddle point that may contain a single sample contour. Determines the sampling density of contours.
    3. Noise threshold: Specifies the smallest contour that may be considered as a symmetric region.
  5. Hovering over them will also tell what they are.
  6. After submitting the job, the user will be redirected to another web page after the computation is over.
  7. On this webpage, the detected symmetrical clusters can be viewed. Various aspects of the clusters can be altered by using the controls on the left of the page. A User will be able to change Opacity, Transparency, Colour, Wireframe Mode, and Visibility using the controls provided. Furthermore, the Background colour and Ambient Light settings of the Scene can also be changed.
  8. An alternate way to toggle through the clusters is by using the Circular Knob placed at the top of the web page.
  9. If you are wondering what the "Others" cluster displays, it is simply all the surfaces, where Symmetry was not detected.
  10. Additionally, a widget for monitoring the performance of the graphical display is displayed towards the left of the webpage. Here, there are three options:
    1. FPS Frames rendered in the last second. (The higher the number the better)
    2. MS Milliseconds needed to render a frame. (The lower the number the better)
    3. MB MBytes of allocated memory. (Run Chrome with --enable-precise-memory-info)
  11. Please note that we clean our servers often in accordance to the traffic we receive. Therefore, it might not be a good idea to save the link for later viewing. Instead, we suggest the User to download the Zip file from the "Links" section provided.
  12. The downloaded file after extracting will have the following files and folders.
    1. A folder named VTK which contains the files with vtk extensions which can be loaded on the paraview.
    2. A folder named RAW which contains the files with raw extension which can be used for volumetric analysis.
    3. A readme file which explains the user how to use the output data.
    4. The map file of the corresponding dataset (if the EMD Id is specified).
  13. After downloading, the User can again view the detected Symmetry in the browser by setting up a local server. (Run python -m SimpleHTTPServer in the browser directory). Another way to view the detected Symmetry would be to use ParaView.
  14. For loading the clusters into ParaView, we have provided a small Python Script titled "" along with the downloaded files. Simply run this file, to view the clusters in ParaView.
  15. combines all the iso surfaces that form a cluster and loads all the clusters one by one. It also displays the smoothened Iso surfaces. This file can also load all isosurfaces of all clusters individually one by one on execution.
  16. After submitting the job, the user will get a downloadable file after the computation is over. The computatition time depends on the size of the input file.
  17. SymmetryViewer has been tested with Python 2.7, ParaView 3.14, Three.js 82 and VTK 6!

Method overview

Protein complexes often contain repeating patterns at multiple scales. For example, many proteins are composed of copies of a chain occurring multiple times to give the protein its symmetric tertiary structure. This server implements a very efficient method developed by Thomas and Natarajan [1] for determining repeating patterns in 3D scalar fields at multiple scales. An integrated topological and geometric approach is employed to efficiently and automatically determine the symmetries at multiple scales.
This method is applied to electron density maps available from the Electron Microscopy Data Bank (EMDB).

[1] Dilip Mathew Thomas and Vijay Natarajan. Detecting symmetry in scalar fields using augmented extremum graphs. IEEE Transactions on Visualization and Computer Graphics (IEEE SciVis 2013), 19 (12), 2013, 2663-2672.

Precomputed Examples


Volume rendering of Cryo-EM dataset EMDB-1134
Volume rendering of Cryo-EM dataset EMDB-1654
Volume rendering of Cryo-EM dataset EMDB-1603

Influence of parameters

Influence of Stabilization parameter in EMDB-1292
Influence of approximation parameter in EMDB-1734
Influence of Stabilization parameter in EMDB-1706

About us

Dilip Thomas
Ph.D., Dept. of CSA,IISc
Vijay Natarajan
Associate Professor, Dept. of CSA,IISc
Research assistant, Dept. of CSA,IISc
Adhitya Kamakshidasan
Intern, NNMCB

Contact Us

For suggestions, comments and feedback: [AT] iisc [DOT] ac [DOT] in

© Visualization and Graphics Lab, CSA, IISc