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

PURPOSE

Searches for local density peaks in a volume and stores the output in document file.

SEE ALSO

PK	[Peak search]
PK 3	[Peak search - 3D]
PK C	[Peak search - Center of gravity]
PK D	[Peak search - output to Document file]
PK DC	[Peak search - Center of gravity, output to Document file]

USAGE

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

[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: REC001
[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:+]

.ENTER # 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 then asks for the next two specifications:

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

.Z RADIUS OF ELLIPSES: 4.5
[Enter the Z radius for the center of gravity calculations]

If 'Center of Origin' override option was chosen, SPIDER asks for the next TWO specifications:

.X,Y ORIGIN COORDINATES: 12,15

.Z ORIGIN COORDINATE: 11
[Enter the new origin coordinates.]

.ENTER 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]

NOTES

1. Memory required: 3*NX*NY+7*(Number of peaks requested)

SUBROUTINES

SPEAK3, PKSR3, CGR_3

CALLER

UTIL1