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===== 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: [[http://blake.bcm.edu/dl/EMAN2/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: [[http://blake.bcm.edu/dl/EMAN2/1XCK_chain.pdb]]
  * Mm-cpn structure: [[http://blake.bcm.edu/dl/EMAN2/3LOS_chain.pdb]]
  * RyR structure [[http://blake.bcm.edu/dl/EMAN2/2XOA.pdb]]
  * Ribosome EF structure [[http://blake.bcm.edu/dl/EMAN2/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