SPIDER: PK 3D (Peak search - 3D, output to Document file)

PK 3D - Peak search - 3D, output to Document file

(6/6/13)

PURPOSE

Searches for local density peaks in a volume and stores the output in document file. Does NOT find "maximum" location when image has plateaus. It may even find the "last" value along the plateau! To overcome this, low pass filter the volume first. Example.

SEE ALSO

PK 3R	[Peak search - 3D, Restricted neighborhood, output to Document file]
PK	[Peak search]

USAGE

.OPERATION: PK 3D [x],[y],[z],[xf],[yf],[zf],[pk]

[Find peak info. This operation can return up to 7 optional register variables which contain info on the highest peak:

Variable	Example	Receives
First	[x]	Peak X location (integer)
Second	[y]	Peak Y location (integer)
Third	[x]	Peak Z location (integer)
Fourth	[xf]	Peak X subpixel location
Fifth	[yf]	Peak Y subpixel location
Sixth	[xf]	Peak Z subpixel location
Seventh	[pk]	Peak height

[The first three register variables receive the integer coordinates of the highest peak, the next three register variables receive the floating point coordinates calculated within a 3x3x3 box. The last register variable receives the absolute height of the peak.]

.INPUT FILE: VOL001
[Enter the name of the file containing the volume.]

.MAXIMA(+) OR MINIMA(-)?: +
[Enter '+' if you want the local maxima and '-' if you want the local minima. Default is: '+'.]

.NUMBER OF PEAKS, CENTER ORIGIN OVERRIDE (1/0): 80,0
[Enter the number of maxima or minima sought. The default origin is assumed at the volume's center (NX/2 + 1, NY/2 + 1, NZ/2 + 1). If a different origin position is desired, enter '1' in the second position. The system will then allow you to enter the x,y,z coordinates of the origin to be used. In addition, a reference peak may be specified, and the ratio of the height of each data peak to this peak value will be calculated. Default reference peak number is 1.]

.CENTER OF GRAVITY CALCULATION? (Y/N): N
[Answer 'N' if only simple peak search is requested.]

If the answer is 'Y' SPIDER asks:

.X, Y, & Z RADII OF ELLIPSES: 5.3, 4.5, 4.5
[Enter the X, Y & Z radii of the ellipses determining the spatial region around the highest peak where the center of gravity is going to be calculated.]

If 'Center of Origin' override option was chosen, SPIDER asks the next two questions:

.X, Y, & Z ORIGIN COORDINATES: 1, 1, 1
[Enter the new origin coordinates.]

.PEAK NUMBER FOR RATIO: 1
[Enter the number of the peak relative to which the heights of the other peaks are calculated. This ratio is printed out and listed in the document file along with the other parameters of the peaks.]

.BOX SELECTION (Y/N): Y
[Enter 'Y' if you want to confine the search within a box smaller than the 3-D volume.]

If 'Y' is specified, SPIDER asks the next three questions:

.LOWER,UPPER SLICE: 10,50
[Enter lower and upper Z coordinates of confining box]

.LOWER,UPPER ROW: 0,60
[Enter lower, upper Y coordinates of confining box.]

.LOWER,UPPER SAMPLE: 12,48
[Enter lower, upper X coordinates of confining box.]

.DOCUMENT FILE: DOC001
[Enter name of output document file. Enter '*' if no document file is wanted.]

CALLER

UTIL1