Surface

Purpose

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 viewed along the nsam axis, thus the view is nrow x nslice.

User can specify:

Surface level (threshold).

Relative contribution from depth versus 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. Rotate the output from step 1. again using RT 3D with Euler angles: PHI = 90, THETA = 90 and PSI = 180. (We will simplify this is the new Java Web.)

    3. source: surface.html     last update: 2/11/2002     ArDean Leith