== Segger ==
=== Wed AM Practical ===
Segger is a tool for segmenting density maps and for quick rigid-body docking of structures into density maps [1].

The software is distributed as part of Chimera which will already be installed for the workshop.

'''Segmentation'''

Data: dowload the following files and place the in the same directory (in the tutorial, that directory will be referred to as the segger_data directory). Alternatively, download all the files in a zip file: [[attachment:segger_data.zip]].

 * GroEL at 11.5Å resolution: [[ftp://emdb.rutgers.edu/structures/EMD-1080/map/emd_1080.map.gz|emd_1080.map.gz]]
 * GroEL at 4.2Å resolution: [[ftp://emdb.rutgers.edu/structures/EMD-5001/map/emd_5001.map.gz|emd_5001.map.gz]]
 * Mm-cpn at 4.3Å resolution: [[ftp://emdb.rutgers.edu/structures/EMD-5137/map/emd_5137.map.gz|emd_5137.map.gz]]
 * RyR at 9.6Å resolution: [[ftp://emdb.rutgers.edu/structures/EMD-1275/map/emd_1275.map.gz|emd_1275.map.gz]] 
 * Ribosome at 6.4Å resolution: [[ftp://emdb.rutgers.edu/structures/EMD-5030/map/emd_5030.map.gz|emd_5030.map.gz]]

'''Rigid-body Docking'''

Data:

 * GroEL structure: [[attachment:1XCK_chain.pdb]]
 * Mm-cpn structure: [[attachment:3LOS_chain.pdb]]
 * RyR structure [[attachment:2XOA.pdb]]
 * Ribosome EF structure [[attachment:ribosome_EF.pdb]]

'''References'''

[1] Pintilie, G., Zhang, J., Goddard, T., Chiu, W., Gossard, D. Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions, Journal of Structural Biology 170(3), pp 427-438, 2010