Diff for "Ws2011/Segger"

Differences between revisions 11 and 12

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 provided as part of Chimera which will already be installed for the workshop.

Segmentation

Data:

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
Mm-cpn at 8.0Å resolution: emd_5140.map.gz
Ribosome at 6.4Å resolution: emd_5030.map.gz
Rotavirus at 3.8Å resolution: emd_1461.map.gz

Rigid-body Docking

Data:

GroEL structure: 1xck.pdb
Mm-cpn structure: 3los.pdb
Ribosome structure: 1vsa.pdb, 2ow8.pdb
Rotavirus structure: 1qhd.pdb

Here is some sample data to download:segger_demo_2011.tgz

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

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+   ← Revision 12 as of 2011-03-01 23:07:49 → ⇥
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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]]