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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 ]
... 60000 asymmetric units for this C2 point-group symmetry structure (Grant et al., 2011). 19.9.6. Parallel automatic particle picking | | Parallel ... resolution. AcknowledgementsWe acknowledge recent financial support from the EU/NOE (grant No. NOE-PE0748), from the Dutch Ministry of Economic Affairs (Cyttron project No. BIBCR_PX0948) and from the BBSRC (grant No. BB/G015236/1). We thank all users ...

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 ]
... Gowen, B., Matadeen, R., Orlova, E. V., Finn, R., Pape, T., Cohen, D., Stark, H., Schmidt, R., Schatz, M. & Patwardhan, A. ...

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 ]
Handling multiple 3D reconstructions in parallel 19.9.9. Handling multiple 3D reconstructions in parallel A new parallel 3D reconstruction program was created based on the earlier ex-core program implementing the `exact filter' algorithm (Harauz & van Heel, 1986). With all 3D reconstructions now organized in in-core subroutines, the new program ...

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 ]
... Gowen, B., Matadeen, R., Orlova, E. V., Finn, R., Pape, T., Cohen, D., Stark, H., Schmidt, R., Schatz, M. & Patwardhan, A. ...

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 ]
... Gowen, B., Matadeen, R., Orlova, E. V., Finn, R., Pape, T., Cohen, D., Stark, H., Schmidt, R., Schatz, M. & Patwardhan, A. ... protein synthesis. Nature (London), 427, 862-865. Spahn, C. M. T. & Penczek, P. A. (2009). Exploring conformational modes of macromolecular ...

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 ]
Parallel automatic particle picking 19.9.6. Parallel automatic particle picking Parallel processing is of increasing importance for collecting the large raw data sets required for 4D cryo-EM. If we are interested in a structure that represents 1% of all molecular complexes, we need to increase the size of the data set ...

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 ]
... 60000 asymmetric units for this C2 point-group 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 ]
... Gowen, B., Matadeen, R., Orlova, E. V., Finn, R., Pape, T., Cohen, D., Stark, H., Schmidt, R., Schatz, M. & Patwardhan, A. ...

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 ]
IMAGIC `4D' processing/data format 19.9.3. IMAGIC `4D' processing/data format Recently, another major overhaul of the system was undertaken in order to better handle three-dimensional structural heterogeneity. The relevant IMAGIC programs can now loop over entire three-dimensional volumes (and not just two-dimensional images) allowing programs to tackle ...

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 ]
The IMAGIC software 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 30 years of continuous developments, including various major redesign phases. It was one of the first software packages in electron microscopy and many now ...

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