VO MD - Vector Operation - angular Document file from 'AP MD' output

(10/12/12)

PURPOSE

Convert output document file from the 'AP MD', 'AP RD', or 'AP RN' operation to an angular document file containing three Eulerian angles. OBSOLETE, not needed if you use 'AP SH' instead of the obsolete 'AP MD' operation

SEE ALSO

VO EA [Vector Operation - Create Doc File Containing Evenly Spaced Angles]
VO RA [Vector Operation - Rotate Angular doc file]
AP MD [Alignment - Multi reference, rotation ||]
AP SH [Alignment - multi-reference, exhaustive rotation & shift ||*]

USAGE

.OPERATION: VO MD

.ANGULAR DOCUMENT FILE NAME: REFANG
[Enter the name of the reference angles document file (created by 'VO EA') used to calculate reference projections required for 'AP MD', etc.]

.OUTPUT FROM AP MD/RD/RN DOCUMENT: APMD101
[Enter the name of the document file produced by the 'AP MD' command. This document file should contain 6 columns:

1.Number of the most similar reference projection. When this number is negative the most similar is a mirrored projection (see appended SPIDER procedure). When this number is zero, the line is skipped and the output angular document file will not contain corresponding key.

2.Distance. Can be used as a similarity measure. Output from 'AP MD' document.

3. "-psi" angle. In-plane rotationangle determined.

4. Always 0.0

5. Always 0.0

6. Experimental projection number.

.DOCUMENT: OUTANGLES
[Enter the name for the angular document file that will be produced. This document file will contain three columns with the three Eulerian angles psi, theta, and phi. The key numbers will correspond to experimental projection numbers from column 6 of the 'AP MD', 'AP RD', 'AP RN' output document file. Thus, for image file series with gaps the keys will not be consecutive. Moreover, for the output files from AP RD/RN operations the entries for non-matching projections (marked by 0 in the first column) will be omitted. The angular document file can be subsequently used in the 'BP RP' operation to calculate a refined 3D reconstruction.]

NOTES

  1. In 3D space the projection with the direction (psi, theta, phi) has its mirrored [around X-axis] counterpart in the direction:
    (-psi, 180-theta, phi+180).
    To save time, the operation 'AP MD' takes this into account, and each data projection is compared with the reference projection and its mirrored version at the same time. Thus, only half of the total number of reference projections are required, namely, only those with 0<theta<90.
    If the best match was with the mirrored reference projection, then the number stored in the first column of the document file is equal to the number of the corresponding mirrored reference projection plus an offset equal to the total number of reference projections.

  2. Implemented by P. Penczek

SUBROUTINES

VOMD

CALLER

DRIV1

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