Content-type: text/html Manpage of modTwist2EM

modTwist2EM

Section: User Commands (1)
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NAME

modTwist2EM - Estimate fiber twist from center and surface contours  

SYNOPSIS

modTwist2EM modelFilename referenceParticleNum referenceContourNum  

DESCRIPTION

When aligning and averaging particles along a twisted fiber, a faster, more limited, and potentially more accurate initial search can be used if the fiber twist can be estimated beforehand. This can also help greatly in reducing or eliminating missing wedge artifacts. ModTwist2EM performs such estimation given an IMOD model containing points along the center of the fiber and corresponding points on the surface to indicate the twist. The output is a new model (named "_Twisted.mod") and an initial motive list (named "RefP<n>_initMOTL.csv") where <n> is the number of the particle chosen as a reference. Models used as input to modTwist2EM must satisfy several requirements.
1) The model must contain exactly 2 objects. Object 1
represents the center of the fiber, and object 2 the surface.
2) The contours and particles in object 1 must be in exact 1-to-1
correspondence with those in object 2, and particles must be in order of increasing axial distance from particle 1 in contour 1.
3) Each particle in object 1 should be, an nearly as possible, at
the same axial position as the corresponding particle in object 2. Small, inadvertent errors during modeling will be compensated for automatically, but large discrepancies will cause nonsensical results.
4) If multiple contours are present, adjacent contours should overlap
by exactly one point. I.e. in object 1, the last point in contour N should be at the same axial position as the first point in contour N + 1. In some cases, this may not be possible. It is acceptable for the last point in contour N and the first point in contour N + 1 to have similar, but not identical axial positions as long as you are aware of the consequences. First, any twist in the fiber axis between these 2 locations must be insignificant compared to jump in twist angle between the contours. ModTwist2EM will attribute the difference entirely to the latter cause. Second, the last point in contour N will always be omitted from the output when there is a subsequent contour to prevent duplicate points.

When modeling microtubules, for example, individual protofilaments can often be traced for some distance in a tomogram, until they become indistinct due to missing tomographic information. In this case, separate contours would be created in the input model for each protofilament traced. Of course, it is also permissible to break contours even when not changing protofilaments... e.g. to skip over and artifact. ModTwist2EM estimates fiber twist by computing the rotation of object 2 points around the axis determined by object 1 points within each contour. The overlap between adjacent contours is required to smoothly transition between contours when multiple contours are present. This duplication is not carried over to the output model, and will not bias PEET as a result. ModTwist2EM is often run immediately after addModPts, although this is not required. (If addModPts is to be used, it must be run prior to modTwist2EM).

 

AUTHORS

Rick Gaudette
Quanren Xiong
John Heumann  

SEE ALSO

PEET(1), addModPts(1)


 

Index

NAME
SYNOPSIS
DESCRIPTION
AUTHORS
SEE ALSO

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Time: 21:10:05 GMT, March 20, 2017