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| Segger is a tool for segmentind density maps, and for quick rigid-body docking of structures into density maps [1]. | Segger is a tool for segmenting density maps and for quick rigid-body docking of structures into density maps [1]. |
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| The software is provided as part of Chimera which will already be installed for the workshop. | The software is distributed as part of Chimera which will already be installed for the workshop. |
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| Data: | 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]]. |
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| * GroEL at 10.0Å resolution: [[ftp://emdb.rutgers.edu/structures/EMD-1080/map/emd_1080.map.gz|emd_1080.map.gz]] | * GroEL at 11.5Å resolution: [[ftp://emdb.rutgers.edu/structures/EMD-1080/map/emd_1080.map.gz|emd_1080.map.gz]] |
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| * Mm-cpn at 8.0Å resolution: [[ftp://emdb.rutgers.edu/structures/EMD-5140/map/emd_5140.map.gz|emd_5140.map.gz]] | * RyR at 9.6Å resolution: [[ftp://emdb.rutgers.edu/structures/EMD-1275/map/emd_1275.map.gz|emd_1275.map.gz]] |
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| * Rotavirus at 3.8Å resolution: [[ftp://emdb.rutgers.edu/structures/EMD-1461/map/emd_1461.map.gz|emd_1461.map.gz]] | |
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| * GroEL structure: [[http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1XCK|1xck.pdb]] * Mm-cpn structure: [[http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3LOS|3los.pdb]] * Ribosome structure: [[http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1VSA|1vsa.pdb]], [[http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=2OW8|2ow8.pdb]] * Rotavirus structure: [[http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1QHD|1qhd.pdb]] Here is some sample data to download:[[attachment:segger_demo_2011.tgz]] |
* 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]] |
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: segger_data.zip.
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