Differences
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localfsc [2015/09/04 15:05] 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. | ||
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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. | ||