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OR 3 - ORient in 3 dimensions

(1/15/97)

PURPOSE

Determines orientation of best match between two volumes or 3D auto-correlation functions within angular search ranges determined by the user. Eulerian angles alpha, beta, and gamma are independently determined in an iterative approach.

SEE ALSO

OR [orient, data on half circle used]
OR 3MM [orient with 32x32x32 or 64x64x64]
OR 3Q [orientation search in 3-D]
OR FM [orient, data on full circle used, > one peak]
OR M [orient, find more than one peak]
OR P [orient data]
OR F [orient, data on full circle used]

USAGE

.OPERATION: OR 3,X10,X11,X12,X13,X14,X15

[The optional output registers X10 through X15 contain alpha, beta, gamma, the angles of best fit, and rho(alpha), rho(beta), rho(gamma), the values of the mean weighted correlation coefficients associated with these angles.

.INPUT FILE: VOL001
[Enter name of the file containing the volume or 3D ACF to be matched with the reference]

.REFER FILE: VOL002
[Enter name of the file containing the reference volume or ACF]

.ALPHA START, INCREMENT: -15., 1.
[enter for alpha the starting value and the increment in degrees]

.NUMBER OF ALPHAS: 30
[enter the number of alphas to be used]

.BETA START, INCREMENT: -10., 2.
[enter for beta the starting value and the increment]

.NUMBER OF BETAS: 10
[enter the number of betas to be used]

.GAMMA START, INCREMENT: -15., 1.
[enter for gamma the starting value and the increment]

.NUMBER OF GAMMAS: 30
[enter the number of gammas to be used]

.NUMBER OF PLOTS/PAGE (1..10): It allows choosing of number
of plots to be drawn in the same page (usefull when there are large differences between radial plots).

.RADIUS MINIMUM, MAXIMUM: 10, 18
[Radii of the shells to be considered in the search. These must be specified as integers]

.WEIGHTS? (Y/N): Y
[enter 'Y' if you wish to specify a weight (0 < w <= 1.) for each radius, 'N' if you want to use the default assignment of w=1 for each radius.]

If 'Y' was specified, the system will solicit a weight for each radius. The sequence is

RADIUS = 10
.ENTER WEIGHT: 0.5
RADIUS = 11
.ENTER WEIGHT: 0.75

etc.

For either 'Y' or 'N', the system proceeds as follows:

.STOP WHEN CC DECREASES? (Y/N): Y
[If answered with 'Y', the program will stop the search for each angle in its search range as soon as the first local maximum is encountered (criterion: values of rho for the two following angle increments are smaller than for the current one). If answered with 'N' or <CR>, the entire angular range specified is searched each time.]

.CENTROSYMMETRY? (Y/N): N
[If anwered with 'Y', only half the volume will be considered in the search. This option would always be used for 3D ACF files.]

NOTES

  1. The Eulerian angles are used as defined in "Fundamental Formulas Of Physics", ed. D.H. Menzel, Vol I, p. 91. The angles alpha and beta have the same meaning as the angles used in other SPIDER programs, such as the operation PJ 3 (projection).

  2. The iterative search approach is essentially the same as the one implemented by Knauer et al. (J. Mol. Biol.

  3. , except that in our case the search is performed shell by shell, thus permitting the specification of a range of radii and weights.

  4. The accuracy of this matching is usually high, specially for beta, while there is a tendency to overestimate alpha due to its similarity to the total rotation perpendicular to the optical axis.

SUBROUTINES

CC3DA, ROT3, ROT32

CALLER

UTIL3

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