- 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 Data Analysis
- Overview of dimension reduction and classification with procedures.
- Classification
- Supervised vs unsupervised classification.
- Classification and Clustering Tutorial.
- Tutorial on classification and clustering techniques.
- Supervised Classification.
- Supervised classification techniques.
- 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.
- Particle Verification using Classification
- Accompanies "Projection Matching" batch files above.
- 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.