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Techniques Index


2D Techniques
Contrast Transfer Function Correction
Correcting for the transfer function of a microscope.

Particle Picking from Micrographs
Methodology for picking/boxing particles from a micrograph.

Alignment
Alignment strategies for 2D particles.

Reference-free Alignment
Theoretical information on reference-free alignment.

Multvariate Statistics Methods
Overview of dimension reduction and classification with procedures

Classification and Correspondence Analysis
Supervised vs unsupervised classification, and a tutorial on classification, clustering and correspondence analysis

Correlation Averaging
Introduction to quasi-optical filtration and correlation averaging of crystalline lattices using both global and patchwork averaging.

3D Techniques

Strategies for 3D reconstruction
Strategies for 3D reconstruction of macromolecules existing as single particles.

Projection Matching
Methodology for 3D reconstruction using reference projections.

Random Conical (1) and Random Conical (2)
Two different methodologies for random conical tilt reconstruction.

Tomography and Serial-section Reconstruction
Procedures for electron tomography, serial-section reconstruction, and related visualization methods.

RNA versus protein separation
Procedures for segmenting RNA and protein from a ribosome reconstruction.

Difference Maps
Ligands can be isolated by creating a difference map, the subtraction of one volume from another.

Fourier amplitude correction based on low-angle X-ray scattering data
Correction of the amplitude falloff of the final reconstruction in Fourier space, by reference to low-angle X-ray solution scattering.

Icosahedral Reconstruction
Procedures for icosahedral reconstruction.

Segmentation Using SPIDER
Using SPIDER in Segmenting Volumes.

Using SPIDER on Parallel Clusters

Using PubSub
Using PubSub to run single particle alignment, iterative refinement, tomographic double tilt back projection, and tomographic single tilt back projection on a Cluster.

General Techniques for SPIDER on Parallel Clusters.
Techniques for using SPIDER operations to control parallel processing.

IBM SP clusters with LoadLeveler
Techniques for running SPIDER on IBM SP parallel systems using LoadLeveler.

Miscellaneous

RAMOS (RApid MOtif Search) / Signature Search / Motif Search / Docking
Search for location of a motif within a volume
TF SIM supplemental material
Plots of Complex Atomic Scattering Amplitude VS Spatial Frequency

Source: techniques.html     Page updated: 08/09/07     ArDean Leith


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