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localfsc [2015/09/04 14:52] gcardone |
localfsc [2019/06/19 16:22] (current) |
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<WRAP center round info 75%> | <WRAP center round info 75%> | ||
- | Local resolution analysis of the entire map can be done, using the same methodological approach, with programs from [[http://lsbr.niams.nih.gov/bsoft/|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. | + | Local resolution analysis of the entire map can be done, using the same methodological approach, with programs incorporated into [[http://lsbr.niams.nih.gov/bsoft/|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. |
</WRAP> | </WRAP> | ||
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* If you don't already have a directory on your computer that is specific for external plugins for chimera, create one. | * If you don't already have a directory on your computer that is specific for external plugins for chimera, create one. | ||
- | * Download the file [[http://cryoem.ucsd.edu/programs/code/LocalFSC_chimera.tar.gz|LocalFSC_chimera.tar.gz]] in this directory and uncompress it. | + | * Download the file [[http://bakerlab.ucsd.edu/programs/code/LocalFSC_chimera.tar.gz|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. | * 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. | + | The LocalFSC module will be under the Tools->Volume Data menu. |
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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. | 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 [[http://cryoem.ucsd.edu/programs/code/TestCaseLFSC.tar.gz|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. | + | In order to get familiar with the module, here is provided a [[http://bakerlab.ucsd.edu/programs/code/TestCaseLFSC.tar.gz|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 | + | * Uncompress the data. |
- | * Open the tree maps and the marker file in Chimera | + | * Open the tree maps and the marker file in Chimera. |
- | * | + | * Verify that all three maps are overlapping and their pixel size is properly set in the Features->Coordinates menu of the Volume Viewer dialog window. |
- | ------------------------- | + | * Hide the two half maps. |
+ | * Open the module (Tools->Volume Data->LocalFSC in the main window or Tools->LocalFSC in Volume Viewer). | ||
+ | * In Settings, point the first and second map to the two half maps. | ||
+ | * Still in Settings, set the maximum resolution available (i.e. unfiltered out) in the half maps (in this case 10). | ||
+ | * In the main window, select one of the markers with Ctrl-left click and the press the Estimate button in Resolution. The estimate will be listed in the GUI, and the FSC plot will be shown in a separate window. | ||
+ | * You can select multiple markers where to estimate the resolution. In this case the program will not show their corresponding FSC plots. | ||
===== Credits ===== | ===== Credits ===== |