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| Segger is a tool for segmenting density maps and for quick rigid-body docking of structures into density maps [1]. | |
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| Segger is a tool for ... | The software is distributed as part of Chimera which will already be installed for the workshop. |
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| The software is provided as part of Chimera which will already be installed for the workshop. | '''Segmentation''' |
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| Here is some sample data to download: [[attachment:segger_demo_2011.tgz]] |
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 from this [[attachment:segger_data.zip|link]]. |
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| etc. | * 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: [[emdb.rutgers.edu/structures/EMD-1275/map/emd_1275.map.gz|emd_1275.map.gz]] * Ribosome at 6.4Å resolution: [[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 |
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 from this link.
GroEL at 11.5Å resolution: emd_1080.map.gz
GroEL at 4.2Å resolution: emd_5001.map.gz
Mm-cpn at 4.3Å resolution: emd_5137.map.gz
RyR at 9.6Å resolution: emd_1275.map.gz
Ribosome at 6.4Å resolution: emd_5030.map.gz
Rigid-body Docking
Data:
GroEL structure: 1XCK_chain.pdb
Mm-cpn structure: 3LOS_chain.pdb
RyR structure 2XOA.pdb
Ribosome EF structure 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