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12.24 The SAXSPDBFast McXtrace Component
Release: McXtrace 1.0
A sample describing a thin solution of proteins using linear interpolation to increase computational speed. This components must be compiled with the -lgsl and -lgslcblas flags (and possibly linked to the appropriate libraries).
Identification
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Author: Martin Cramer Pedersen (mcpe@nbi.dk) and Søren Kynde (kynde@nbi.dk)
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Origin: KU-Science
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Date: May 2, 2012
Description
This components expands the formfactor amplitude of the protein on spherical harmonics and computes the scattering profile using these. The expansion is done on amino-acid level and does not take hydration layer into account. The component must have a valid .pdb-file as an argument.
This is fast implementation of the SAXSPDB sample component.
Input parameters
Parameters in boldface are required; the others are optional.
|
Name |
Unit |
Description |
Default |
|
|
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|
RhoSolvent |
Å |
Scattering length density of the buffer. |
9.4e-14 |
|
Concentration |
mM |
Concentration of sample. |
0.01 |
|
AbsorptionCrosssection |
1/m |
Absorption cross section of the sample. |
0.0 |
|
xwidth |
m |
Dimension of component in the x-direction. |
|
|
yheight |
m |
Dimension of component in the y-direction. |
|
|
zdepth |
m |
Dimension of component in the z-direction. |
|
|
SampleToDetectorDistance |
m |
Distance from sample to detector (for focusing the scattered x-rays). |
|
|
DetectorRadius |
m |
Radius of the detector (for focusing the scattered x-rays). |
|
|
qMin |
Å\(^{-1}\) |
Lowest q-value, for which a point is generated in the scattering profile |
0.001 |
|
qMax |
Å\(^{-1}\) |
Highest q-value, for which a point is generated in the scattering profile |
0.5 |
|
NumberOfQBins |
|
Number of points generated in inital scattering profile. |
200 |
|
PDBFilepath |
|
Path to the file describing the high resolution structure of the protein. |
”PDBfile.pdb” |
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Links
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Component source code found in file SAXSPDBFast.comp.
