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localfsc [2015/09/04 14:52] gcardone |
localfsc [2015/09/04 15:07] gcardone |
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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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| * 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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| 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://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. | ||
| - | * 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 ===== | ||