Determines defocus parameters from images of untitled specimens, as well as defocus and tilt parameters from images of tilted specimens. CTFFIND is a package that uses images collected using modern technologies such as dose fractionation and phase plates. Defocus parameters are estimated by fitting a model of the microscope’s contrast transfer function (CTF) to an image’s amplitude spectrum.
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Permits surface rendering, multivariate statistical analysis (MSA), automatic classification, projection matching, angular reconstitution, automatic particle selection. IMAGIC can be employed for real data processing run for educational or testing purposes. This tool can exploit the properties of cheap graphic processors. It is useful for 4D analysis at atomic resolution or for refining towards multiple 3D structures.
Describes the reconstruction of biological molecules from the electron micrographs of single particles. SPIDER is an open source project that manages computation using the image-processing software and can also using a graphical user interface (GUI), termed the SPIDER Reconstruction Engine. These two approaches are described to obtain an initial reconstruction: random-conical tilt and common lines.
Calculates and refines three-dimensional (3D) structures of macromolecular assemblies that are calculated from images collected on an electron microscope. Frealign provides a fast and accurate projection matching algorithm, and calculates 3D reconstructions that are fully corrected for the contrast transfer function (CTF) of the microscope. Other features include refinement of microscope defocus and magnification, correction for the Ewald sphere curvature, processing of helical particles, 3D classification, and density masking. Furthermore, algorithms and run scripts were developed to take advantage of parallel computing environments to speed up processing.
Allows particle picking and contrast transfer function (CTF) estimation from cryo-electron microscopy data (cryo-EM). e2boxer.py includes several features: Interactive particle picking, automated particle picking using Gauss convolution method, command-line (batch) automated particle picking (no GUI) using Gauss convolution method and CTF estimation in both GUI and command-line mode.
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Discover our proposed protocols.
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They are easy to use or edit to meet your needs.
Structure of the Bacterial Sex F Pilus Reveals an Assembly of a Stoichiometric Protein Phospholipid Complex
Tools (3):
SPIDER, CTFFIND, FSC
Topics (2):
cryo-EM, Bacterial Infections
Cryo EM structures of Tau filaments from Alzheimer’s disease brain
Tools (3):
MotionCor2, Gctf, RELION
Topics (7):
cryo-EM, Homo sapiens, Brain Diseases, Tauopathies, Brain Diseases, Neurodegenerative Diseases, Plaque, Amyloid
Structure of a zosuquidar and UIC2 bound human mouse chimeric ABCB1
Tools (3):
MotionCor2, Gctf, RELION
Topics (8):
cryo-EM, Homo sapiens, Mus musculus, Neoplasms, Ribonucleotides, Heterocyclic Compounds, 2-Ring, Purine Nucleotides, Nucleotides
Structure and mechanism of the two component α helical pore forming toxin YaxAB
Tools (3):
RELION, MotionCor2, Gctf
Topics (1):
cryo-EM
Assembly and Architecture of the EBV B Cell Entry Triggering Complex
Tools (3):
CTFFIND, SPIDER, UCSF Chimera
Topics (1):
cryo-EM