Difference between revisions of "Filament model"
| Line 1: | Line 1: | ||
| − | Filament models are used for geometries where location and orientation of particles 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. |
| Line 15: | Line 15: | ||
===<tt>filamentWithTorsion</tt>=== | ===<tt>filamentWithTorsion</tt>=== | ||
| − | Parameters | + | The subunits will be defined along the backbone. The center of each subunit will be defined in the backbone, and |
| + | Parameters: | ||
* <tt>dz</tt> distance of the subunits along the backbone (in pixels) | * <tt>dz</tt> distance of the subunits along the backbone (in pixels) | ||
| − | *<tt> dphi</tt> angular distance between the subunits (in degrees) | + | *<tt> dphi</tt> angular distance between the subunits (in degrees). |
| + | * fdf | ||
| + | |||
===<tt>filamentSubunitsObHelix</tt>=== | ===<tt>filamentSubunitsObHelix</tt>=== | ||
| − | Parameters | + | Parameters: |
* <tt>dz</tt> distance of the subunits along the backbone (in pixels) | * <tt>dz</tt> distance of the subunits along the backbone (in pixels) | ||
*<tt> dphi</tt> angular distance between the subunits (in degrees) | *<tt> dphi</tt> angular distance between the subunits (in degrees) | ||
* <tt>radius</tt> distance of the subunits to the backbone (in pixels) | * <tt>radius</tt> distance of the subunits to the backbone (in pixels) | ||
Revision as of 15:18, 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
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, and Parameters:
- dz distance of the subunits along the backbone (in pixels)
- dphi angular distance between the subunits (in degrees).
* fdf
filamentSubunitsObHelix
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)
