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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 ]
... particle cryo-electron microscopy (cryo-EM) has established itself as a new structural-biology technique over the last 15 years. Spectacular ... decade from ~10 to sometimes better than ~4, meaning that a de novo structure determination based on single-particle cryo-EM ... of choice for shedding light on the functioning of many a complex biological system. The design of the software instrumentation ...

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 ]
... Heel, 1987; van Heel et al., 2000) one typically assigns a Euler angle orientation to a 2D image by finding its best overall sinogram correlation peaks ... over multiple anchor sets and has thus been upgraded to a 4D level. As a consequence, the Euler program is ...

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 ]
... reconstructions in parallel 19.9.9. Handling multiple 3D reconstructions in parallel A new parallel 3D reconstruction program was created based on the ... needed, for example, for the 4D MSA approaches. It is a perfect match for the 4D MRA (above) and the 4D ... program, apart from the exact filter algorithm, now also features a novel 3D deconvolution algorithm based on the idea that ...

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 ]
... originally introduced to electron microscopy to handle different views of a macromolecule (van Heel & Frank, 1981; Borland & van Heel, 1990; van ... techniques of choice to structure complex, heterogeneous data sets. Today, a wealth of information on MSA techniques is readily available on ... proportional to the square of the number of images in a data set, making it impossible to process more than ...

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 ]
... centred molecular images (Dube et al., 1993) has taken on a new emphasis. An especially useful variant is the rotational alignment ... are still in full development. MRAs are now used as a tool in 4D analysis by generating MRA references from a set of 3D structures rather than just a single ...

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 ]
... required for 4D cryo-EM. If we are interested in a structure that represents 1% of all molecular complexes, we need ... in order to achieve the same resolution we had for a monodisperse data set. This implies that we need to be ... of the frequency range used for discriminating the presence of a particle with respect to the background. The sensitivity of ...

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 ]
... resolution. These programs have been used for the processing of a highly astigmatic data set of the Limulus polyphemus hemocyanin, resulting in a ~4 reconstruction from only 15000 raw molecular images, corresponding to ... al., 2011). References Grant, T., van Duinen, G., Patwardhan, A. & van Heel, M. (2011). Exploiting astigmatism in single ...

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 ]
... critical IMAGIC code (van Heel et al., 2000), mainly using a message passing interface (MPI; Gropp et al., 1994) to take ... that the same code will run on all machines from a single-CPU notebook computer up to large cluster systems with hundreds of CPUs. Recently, a `GPU' library (see www.nvidia.com/object/cuda_ home.html ) has been ...

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 ]
... just two-dimensional images) allowing programs to tackle problems at a much higher level of complexity. About 25 years ago, a radical redesign of the system allowed small two-dimensional images ... than defining some new header parameters. The reason is that a stack of three-dimensional (3D) volumes (a `4D' data ...

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 ]
... selection etc. The basic file format of IMAGIC consists of a header file, to hold image parameters and processing information, and a separate file holding all actual image data. This `stack' format ... do image-processing scripts (which are operating-system dependent). A unique feature of all IMAGIC programs is that all ...

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