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Four-dimensional cryo-electron microscopy at quasi-atomic resolution: IMAGIC 4D
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, ch. 19.9, pp. 624-628 [ doi:10.1107/97809553602060000875 ]
... reasonable resolution [for reviews of the single-particle methods see van Heel et al. (2000) and Frank (2006)]. In recent years ... resolution. 19.9.2. The IMAGIC software system | | The IMAGIC software system (van Heel & Keegstra, 1981; van Heel et al., 1996) is ...

Angular reconstitution 4D refinements
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.10, p. 627 [ doi:10.1107/97809553602060000875 ]
... 19.9.10. Angular reconstitution 4D refinements With the angular reconstitution approach (van Heel, 1987; van Heel et al., 2000) one typically assigns a Euler ...

Handling multiple 3D reconstructions in parallel
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.9, pp. 626-627 [ doi:10.1107/97809553602060000875 ]
... earlier ex-core program implementing the `exact filter' algorithm (Harauz & van Heel, 1986). With all 3D reconstructions now organized in in ... same overall quality as the classical exact filter algorithm (Harauz & van Heel, 1986). References Harauz, G. & van Heel, M. ( ...

MSA and its parallelization
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.8, p. 626 [ doi:10.1107/97809553602060000875 ]
... to electron microscopy to handle different views of a macromolecule (van Heel & Frank, 1981; Borland & van Heel, 1990; van Heel et al., 2000; Frank, 2006; ...

Parallel multi-reference alignments and reference bias
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.7, p. 626 [ doi:10.1107/97809553602060000875 ]
... alignments and reference bias Large multi-reference alignment (MRA) schemes (van Heel & Stöffler-Meilicke, 1985) have been accelerated by some orders ... magnitude with the introduction of MPI parallelization on computer clusters (van Heel et al., 2000), and MRA remains the largest ...

Parallel automatic particle picking
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.6, p. 625 [ doi:10.1107/97809553602060000875 ]
... one of the oldest ones, based on the local variance (van Heel, 1982) in the raw micrographs or CCD images. It is ... picking is a variant of the original variance image detection (van Heel, 1982) which is based on the local standard ...

Full 2D (parallel) astigmatic contrast transfer function correction
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.5, p. 625 [ doi:10.1107/97809553602060000875 ]
... The IMAGIC contrast transfer function (CTF) estimation and correction programs (van Heel et al., 2000) have recently been upgraded to work fully ... symmetry structure (Grant et al., 2011). References Grant, T., van Duinen, G., Patwardhan, A. & van Heel, M. (2011). ...

Software parallelization
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.4, p. 625 [ doi:10.1107/97809553602060000875 ]
... has been placed on the parallelization of critical IMAGIC code (van Heel et al., 2000), mainly using a message passing interface (MPI ... Interface. Scientific and Engineering Computation Series. Cambridge, MA: MIT Press. Heel, M. van, Gowen, B., Matadeen, R., Orlova, E. V., ...

IMAGIC `4D' processing/data format
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.3, pp. 624-625 [ doi:10.1107/97809553602060000875 ]
... with one header record per 2D image in a stack (van Heel & Keegstra, 1981). The main difference is that specific header ...

The IMAGIC software system
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.2, p. 624 [ doi:10.1107/97809553602060000875 ]
... system 19.9.2. The IMAGIC software system The IMAGIC software system (van Heel & Keegstra, 1981; van Heel et al., 1996) is the result of over ...

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