Differences

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--- localfsc [2015/09/04 14:52]
gcardone
+++ localfsc [2015/09/04 15:05]
gcardone
@@ Line 16: / Line 16: @@
   *     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.
@@ Line 24: / Line 24: @@
 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 =====