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auto3dem:documentation:protocols:initial_model [2015/07/08 13:07] gcardone created |
auto3dem:documentation:protocols:initial_model [2019/06/19 16:22] (current) |
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| ====== Generating a starting model ====== | ====== Generating a starting model ====== | ||
| - | Obtaining a reconstructed density map from a set of particles is an iterative process that requires an initial reference volume, typically a low-resolution reconstruction from the same or a similar sample. When a starting model is not available, one can easily be constructed for icosahedral viruses using the program //setup_rmc//, which relies on the **Random Model Computation** (RMC) method. By default, //setup_rmc// will interrogate the particle parameter files in the dat directory and setup the directories and scripts required to generate, by default, 10 random models, using 150 images from at least the 3 furthest-from-focus micrographs. It will generate two scripts to run in sequence: //RMC_run// to launch the random model calculations, and //RMC_cleanup// to remove all intermediate files after completion. //setup_rmc// will also construct a minimal auto3dem input file (with suffix ''_master''), that can be used to launch the full reconstruction after the starting model has been obtained. | + | Obtaining a reconstructed density map from a set of particles is an iterative process that requires an initial reference volume, typically a low-resolution reconstruction from the same or a similar sample. When a starting model is not available, one can easily be constructed for icosahedral viruses using the program //setup_rmc//, which relies on the **Random Model Computation** (RMC) method. |
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| + | Assuming that you have already generated a //dat// subdirectory containing the initial particle parameter files (ending with ''.dat_000''), the simplest procedure is to run three commands | ||
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| + | setup_rmc | ||
| + | ./RMC_run | ||
| + | ./RMC_cleanup | ||
| + | |||
| + | //setup_rmc// will interrogate the particle parameter files in the parameter directory (default=//dat//) and setup the directories and scripts required to generate, by default, 10 random models, using 150 images from at least the 3 furthest-from-focus micrographs. It will generate two scripts to run in sequence: //RMC_run// to launch the random model calculations, and //RMC_cleanup// to remove all intermediate files after completion. //setup_rmc// will also construct a minimal auto3dem input file (with suffix ''_master''), that can be used to launch the full reconstruction after the starting model has been obtained. | ||
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| If you generate an initial model using the Random Model Computation method, please cite: | If you generate an initial model using the Random Model Computation method, please cite: | ||
| - | Yan X., K. A. Dryden, J. Tang, and T. S. Baker (2007) Ab initio random model method facilitates 3D reconstruction of icosahedral particles. J. Struct. Bio. 157:211-225. ([[http://cryoem.ucsd.edu/publication-pdfs/2007b-Yan-etal-JSB.pdf|pdf]]) | + | Yan X., K. A. Dryden, J. Tang, and T. S. Baker (2007) Ab initio random model method facilitates 3D reconstruction of icosahedral particles. J. Struct. Bio. 157:211-225. ([[http://bakerlab.ucsd.edu/publication-pdfs/2007b-Yan-etal-JSB.pdf|pdf]]) |
| </WRAP> | </WRAP> | ||