PJ ST - Projected Surface - Creation

PURPOSE

Create a surface image of a three-dimensional structure. (I suggest you use the Web "Surface" operation instead ie you want to make a shaded surface representation. It uses similar algorithm, can usually rotate the volume, is faster, and can save the output image.)

SEE ALSO

PJ SHAD	[]
PJ COL	[Projected Surface - Coloring]

USAGE

.OPERATION: PJ ST

.3-D FILE: 3DR100
[Enter the file containing the three-dimensional structure.]

.ROTATION AXIS (Y) (=DEF) OR Z: Z
[Enter rotation axis. Z as rotation axis is a lot faster than Y.]

.OUTPUT FILE: SUR001
[Enter the output file name for the surface image.]

.HORIZONTAL DIMENSION OF SURFACE DEPTH BUFFER: 100
[Enter dimension in the X direction. Does not have to be related to volume dimensions.]

.DEPTH FROM, TO: -32,20
[Enter depth range which should be scanned. The center of the three-dimensional structure is at zero depth, corresponding to x-dim/2+1,y-dim/2+1,z-dim/2+1. Negative values are on the near side of the surface, positive values on the far side, with respect to the reference plane.]

.VIEWING ANGLE: 25
[Enter angle, in degrees, between X direction of reference plane and X direction of 3D object.]

.THRESHOLD: 0.25
[Enter the threshold value that defines the surface. The surface is defined by the values higher than a positive threshold value or lower than a negative threshold value.]

.BACKGROUND (0)ZERO,(1)MIN,(2)MAX,(3)LOCAL MIN,(4)LOCAL MAX: 4
[Enter the desired background for those areas in the resulting image where no surface was found. Explanation of options:

0 = Set background to 0. (Option 0 must be used if subsequent shading is to be applied to the surface. Other options will result in a mottled background after shading.)
1 = Set background to the minimum (distance-1 of the surface image).
2 = Set background to the maximum (distance+1 of the surface image).
3 = Set background to minimum and correct for curvature in Y direction.
4 = Set background to maximum and correct for curvature. Options 3 and 4 can be used to reduce the dynamic range of the depth buffer, when e.g. a long curved fiber creates a large depth difference from one end of the volume to the other and thus delicate surface features are obscured.

To obtain the correct contrast, if no shading is being applied, you must scale the final image with -1. Then option '0', '1' or '3' will give a white background; option '2' or '4' a black background.]

If a '3' or '4' was entered, SPIDER asks:

.BOX LENGTH FOR BACKGROUND FILTER: 25
[Enter the box length, in the X direction, for box convolution used in the background correction.]

.BACKGROUND OFFSET: 5
[Enter offset of box-convoluted background. See below for explanation.]

NOTES

1. The background correction calculates the background for each line in the surface image and does a box convolution to low-pass filter this background function. This function is then subtracted from the surface image. The offset is necessary to ensure that all parts of the surface are on the same side of the background (if desired).

2. For a detailed description, see: M. Radermacher & J. Frank (1984) "Representation of three-dimensionally reconstructed objects in electron microscopy by surfaces of equal density", Journal of Microscopy 136:77-85.

3. When the reference plane is placed in the interior, then a cutaway version of the object is computed. However, the flat cutting plane of such a representation frequently shows artifacts. In order to obtain a "clean" cutting plane in the interior, you must create a separate volume from the portion of the volume you wish to represent, and pad ('PD') the new volume by adding at least one additional slice "in front". If oblique representations are needed, then the number of slices to be added in front must accommodate the extra depth.

4. The 'PJ SHAD' operation would normally be used after this operation to make a shaded surface representation.

SUBROUTINES

MRRSURF

CALLER

VTIL2