Appion

h1. Install Grigorieff lab software

The Grigorieff lab at Brnadies provides several individual programs that are used in Appion. See their "main software page":http://emlab.rose2.brandeis.edu/software

h2. Software used in Appion:

h3. Frealign: Refinement of 3D reconstructions using single-particle images

# Grigorieff, N.  2007.  FREALIGN: high-resolution refinement of single particle structures. J Struct Biol. 157:117–125.

# Grigorieff, N.  1998.  Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 A in ice. J Mol Biol. 277:1033-46.

# Wolf, M, DeRosier DJ, Grigorieff N.  2006.  Ewald sphere correction for single-particle electron microscopy. Ultramicroscopy. 106:376-82.

# Stewart, A, Grigorieff N.  2004.  Noise bias in the refinement of structures derived from single particles. Ultramicroscopy. 102:67-84.

h3. Ctffind3 & ctftilt: CTF estimation

# Mindell, JA, Grigorieff N.  2003.  Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol. 142:334-47.

h3. Signature: Particle selection from micrographs

# Chen, JZ, Grigorieff N.  2007.  SIGNATURE: a single-particle selection system for molecular electron microscopy. J Struct Biol. 157:168-73.

h3. Rmeasure: Resolution measurement

# Grigorieff, N.  2000.  Resolution measurement in structures derived from single particles. Acta Crystallogr D Biol Crystallogr. 56:1270-7.

# Sousa, D, Grigorieff N.  2007.  Ab initio resolution measurement for single particle structures. J Struct Biol. 157:201-10.

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