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LocalFSC is a plugin for Chimera to estimate the resolution in selected subregions of a EM map.

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 analyse 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.

Local resolution analysis of the entire map can be done, using the same methodological approach, with programs from Bsoft. Specifically, local analysis and local adaptive filtering can be performed with blocres and blocfilt, respectively. For further information please read the article cited below.


  • If you don't already have a directory on your computer that is specific for external plugins for chimera, create one.
  • Download the file LocalFSC_chimera.tar.gz in this directory and uncompress it.
  • In Chimera, go to Favorites→Preferences, from Category select Tools and add the directory containing the LocalFSC folder to the Locations.

The LocalFSC module should be under the Tools→Volume Data menu.


Once opened, the LocalFSC module, a help button provides all the basic information on how to use it and on all the different options available in the interface.

In order to get familiar with the module, here is provided a Test Dataset to download, which contains a simulated reconstruction of a ribosome (see article below for details). Specifically, the archive file contains three maps (two half maps and one map from all the particles) and a Chimera marker file with two markers pointing to two domains with different occupancy level.

  • Uncompress the data
  • Open the tree maps and the marker file in Chimera



The plugin was developed by Giovanni Cardone. Acknowledgements go to Tom Goddard, UCSF, for revising the code and providing useful insights.


If you find this plugin useful for your research project, please cite:

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. (