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localfsc [2015/09/04 12:12] gcardone created |
localfsc [2019/06/19 16:22] |
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| - | ====== LocalFSC ====== | ||
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| - | LocalFSC is a plugin for Chimera to estimate the resolution in selected subregions of a EM map. | ||
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| - | The resolution is estimated by means of the Fourier Shell Correlation (FSC), calculated from two independent maps. Generally these are the maps each generated from half the particles in a data set. Selection is performed by placing markers in the regions of interest, and the size of the regions to analyze can be set either manually or automatically. Comments can be added to each measure, and all the estimates can be saved in a text file for further analysis. | ||
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| - | ===== Installation ===== | ||
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| - | * Create a new directory that will contain the plugin. | ||
| - | * Download and unzip the file [[http://cryoem.ucsd.edu/programs/code/LocalFSC_chimera.tar.gz|LocalFSC_chimera.tar.gz]] in this new directory. | ||
| - | * Open Chimera and go to Favorites/Preferences. | ||
| - | * Select "Tools" Category and add the directory containing the LocalFSC folder to the "Locations". | ||
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| - | The LocalFSC module now should appear under Tools->Volume Data menu. | ||
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| - | ===== Usage ===== | ||
| - | A test data set is provided together with a tutorial which describes the procedure to get from the raw micrographs to a helical reconstruction. | ||
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| - | [[http://cryoem.ucsd.edu/programs/IHRSR++tutorial_v1.5.pdf|Tutorial]] (pdf) | ||
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| - | [[http://cryoem.ucsd.edu/programs/code/IHRSR_test_prob.tar.gz|Test Dataset]] (**~5 GB file**) | ||
| - | ------------------------- | ||
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| - | ===== Credits ===== | ||
| - | The plugin was developed by Giovanni Cardone. Acknowledgements go to Tom Goddard, UCSF, for revising the code and providing useful insights. | ||
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| - | ===== Citation ===== | ||
| - | If you find this plugin useful for your research project, please cite: | ||
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| - | Cardone G., J. B. Heymann, and A. C. Steven (2013) One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions. J. Struct. Biol. 184:226-236. | ||
| - | ([[http://dx.doi.org/10.1016/j.jsb.2013.08.002]]) | ||
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