Difference between revisions of "Filament model"
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Filament models are used for geometries where location and orientation of particles to be cropped (called ''subunits''in this context) can be defined with relation to tubular estructures. | Filament models are used for geometries where location and orientation of particles to be cropped (called ''subunits''in this context) can be defined with relation to tubular estructures. | ||
| − | The usual way of handling them is by opening a small fraction of a tomogram inside <tt>dtmslice</tt> and mark manually positions that will be used to define a "backbone". Loosely speaking, we call the "''backbone'' of the filament" to the series of ordered points that arise from defining successive orthogonal sections along the path of the filament and picking the central point. Different models are available for the different relationships between the "backbone" of the filament and the locations and positions of the particles to be cropped. | + | The usual way of handling them is by opening a small fraction of a tomogram inside <tt>dtmslice</tt> and mark manually positions that will be used to define a "backbone". Loosely speaking, we call the "''backbone'' of the filament" to the series of ordered points that arise from defining successive orthogonal sections along the path of the filament and picking the central point. Different models are available for the different relationships between the "backbone" of the filament and the locations and positions of the particles to be cropped. |
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==Input stage== | ==Input stage== | ||
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===Clicking input points in <tt>dtmslice</tt>=== | ===Clicking input points in <tt>dtmslice</tt>=== | ||
| + | A [[https://www.youtube.com/watch?v=hsZ-9xAYufI video tutorial]] explains with detail the process of picking points and converting them into subunit locations. | ||
| − | + | ==Geometric computation stage== | |
| − | == | ||
Different models are provided to account for different ways of relating particles to the backbone. | Different models are provided to account for different ways of relating particles to the backbone. | ||
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===<tt>filamentSubunitsOnHelix</tt>=== | ===<tt>filamentSubunitsOnHelix</tt>=== | ||
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| + | In this case, the subunits to be cropped are supposed to be located on a helix that turns along the backbone of the filament. The center of the subunits is on a fixed distance from the backbone of the filament (defined by parameter <tt>radius</tt>), and the ''z'' direction points radially from the backbone, while ''x'' points along the way of the filament. | ||
Parameters: | Parameters: | ||
Revision as of 14:53, 4 August 2016
Filament models are used for geometries where location and orientation of particles to be cropped (called subunitsin this context) can be defined with relation to tubular estructures.
The usual way of handling them is by opening a small fraction of a tomogram inside dtmslice and mark manually positions that will be used to define a "backbone". Loosely speaking, we call the "backbone of the filament" to the series of ordered points that arise from defining successive orthogonal sections along the path of the filament and picking the central point. Different models are available for the different relationships between the "backbone" of the filament and the locations and positions of the particles to be cropped.
Contents
Input stage
The input points in a filament model are used to define a smooth interpolant called backbone.
Clicking input points in dtmslice
A [video tutorial] explains with detail the process of picking points and converting them into subunit locations.
Geometric computation stage
Different models are provided to account for different ways of relating particles to the backbone.
filamentWithTorsion
The subunits will be defined along the backbone. The center of each subunit will be defined in the backbone. The zdirection of the subunit is defined to be colineal with the orientation of backbone at that point, and the distance between two subsequent subunits is defined by the model parameter dz. The torsion effect referred to by the name of the model refers to the fact that the x direction of two subsequent subunits can be chosen to vary a fixed amount (with parameter dphi<subunits>)
Parameters:
- dz distance of the subunits along the backbone (in pixels)
- dphi torsion between subunits (in degrees).
filamentSubunitsOnHelix
In this case, the subunits to be cropped are supposed to be located on a helix that turns along the backbone of the filament. The center of the subunits is on a fixed distance from the backbone of the filament (defined by parameter radius), and the z direction points radially from the backbone, while x points along the way of the filament.
Parameters:
- dz distance of the subunits along the backbone (in pixels)
- dphi angular distance between the subunits (in degrees)
- radius distance of the subunits to the backbone (in pixels)
