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auto3dem:extra_tools [2015/12/22 19:06] gcardone |
auto3dem:extra_tools [2019/06/19 16:22] |
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| - | ====== Auxiliary Programs ====== | ||
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| - | In addition to the main program auto3dem, the package provides additional programs to perform additional processing or analysis. | ||
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| - | ===== a3dm tools ===== | ||
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| - | These are programs all starting with the prefix ''a3dm_'', which mostly support the user during the analysis of the results from running auto3dem. They are all written in python language, and some of them require modules (e.g. numpy, matplotlib, tkinter) that are available on most Linux OS distributions, even if some times they are not installed by default. | ||
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| - | For all of them it is possible to get information on how to use them by simply typing the name of the program, without arguments or with ''--help''. | ||
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| - | === a3dm_plot_fsc === | ||
| - | Plot FSC curves for reconstructions obtained from auto3dem at the given | ||
| - | iteration numbers. Multiple iterations, separated by commas, and/or ranges | ||
| - | (separated by dash) can be specified (examples: 1,4,5 or 1,4-10,5 or 1-11). | ||
| - | Alternatively a list of .agr files can specified with the option -f, giving | ||
| - | complete paths separated by commas but all within apices and using wild cards | ||
| - | (example: 'dat2/test_3.agr,dat/*_2?.agr') | ||
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| - | === a3dm_plot_score === | ||
| - | Plot the score assigned to each particle. Input can be either a configuration | ||
| - | (master/continue) file or a list of orientation parameter (dat) files. | ||
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| - | === a3dm_fsc2xml === | ||
| - | Convert FSC curves to EMDB-compatible XML format. | ||
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| - | === a3dm_dat_stats === | ||
| - | Calculate and display statistics from orientation parameter (.dat) files. | ||
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| - | === a3dm_sel_stableparts === | ||
| - | Select only stable particles, i.e. with unchanged orientation with respect to a previous iteration, and generate a new set of orientation parameter (.dat) files. The inverse selection (i.e. unstable particles) can be done with the flag --inverse. | ||
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| - | === a3dm_icosrotate === | ||
| - | Rotate an icosahedral map from standard orientation to one with a pair of vertices positioned along the z axis. The opposite rotation can be applied using the option ''--inverse''. | ||
| - | The program can be used on a map, a single .dat file or on a master/continue file. In the last case it reads the configuration and applies the rotation to the particles parameters of all the .dat files listed and to the reference map(s). The program automatically identifies which input type is given. Currently, the main limitation is that it is not possible to specify which vertex to place along the z-axis. [[http://cryoem.ucsd.edu/programs/code/emd_5946b6.pif|Here]] is provided a virus map with a connector in the assumed vertex, that can be used to familiarize with the convention used by the program. | ||
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| - | === a3dm_mg_inspect_prepare === | ||
| - | Generate auxiliary info and images for screening micrographs using //a3dm_mg_inspect//. | ||
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| - | === a3dm_mg_inspect === | ||
| - | Quickly inspect and screen micrographs by means of a graphical interface. | ||