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Install Grigorieff lab software » History » Revision 3

Revision 2 (Neil Voss, 05/17/2010 09:34 AM) → Revision 3/18 (Neil Voss, 05/17/2010 09:36 AM)

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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