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Four-dimensional cryo-electron microscopy at quasi-atomic resolution: IMAGIC 4D
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 ~10Å to sometimes better than ~4Å, 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
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
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
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
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
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
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 ~4Å 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
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
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
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 ...
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 ~10Å to sometimes better than ~4Å, 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
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
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
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
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
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
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 ~4Å 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
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
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
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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