Differences

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--- localfsc [2015/09/04 14:27]
gcardone
+++ localfsc [2019/06/19 16:22] (current)
@@ Line 6: / Line 6: @@
 <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>
@@ Line 12: / Line 12: @@
 ===== Installation =====
-  *     If you don't already have a directory on your computer that is specific for external plugins for chimera, create a new 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.
-The LocalFSC module should be under the Tools->Volume Data menu.
+The LocalFSC module will be under the Tools->Volume Data menu.
 ===== 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.
+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.
-[[http://cryoem.ucsd.edu/programs/IHRSR++tutorial_v1.5.pdf|Tutorial]] (pdf)
+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.
-[[http://cryoem.ucsd.edu/programs/code/IHRSR_test_prob.tar.gz|Test Dataset]] (**~5 GB file**)
+  * 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 =====