Web Icon    Web: Surface


Does a fast surface display from a 3D file. Surface is created at a user selected threshold. Surface is viusalized by shining "light" on a tile at the desired surface. Can add depth shading. Can capture surface views while rotating. Volume is NOW viewed along the nslice (Z) axis, thus the view is nsam x nrow.

User can specify:

Surface level (threshold).

Depth shading .

Surface reflectivity.

Scaling or magnification.

Rotation angle.

Rotation Angle convention.
Either Euler angles similar to the convention used in SPIDER or rotations around simple file axes.

Movie creation.
Captures files at specified rotations or thresholds which can be played with the movie operation of Web.

Angle conventions

To make a movie of a SPIDER volume rotating around Z-axis:

  1. Using Surface operation of Web, specifiy Euler angle rotation convention and find the desired starting orientation of the volume.
    (Change the PHI, THETA and PSI values until you get the desired view).
  2. Note the PHI, THETA and PSI values from Web Surface operation for which you get the desired orientation.
  3. Use SPIDER operation: RT 3D to rotate the SPIDER volume to the PHI, THETA and PSI values that you have noted above.
  4. Load the new SPIDER volume (rotated one) in Web and the use Surface operation with Euler angles PHI = 0, THETA = 0 and PSI = 0.
  5. Using the movie toggle in Surface operation, change the value of PHI from 0-360 degrees at the desired intervals and create frames of movie.
To obtain same view as SPIDER PJ 3 shows:

  1. Use RT 3D to rotate the volume with the same euler angles as used for PJ 3

  2. Source: surface.html     Last update: 10/27/2011     ArDean Leith