Software Package Details

Software Name: Segger

Software Licensing: GSL (open source)

Software URL: http://ncmi.bcm.edu/ncmi/software/segger/

Software Reference: See the webpage for detailed references.

Software Capabilities:

  • See the short description.

Software Description:

Segger is available as a plug-in to Chimera, and is included in version 1.5 and the latest daily builds.

It segments a map by first applying the watershed method and then grouping the resulting regions through scale-space filtering or smoothing using a Gaussian kernel. Most of the time regions corresponding to proteins are obtained.

The grouping process produces a hierarchy, which is leveraged in interactive modification of the results. Ungrouping breaks up a region into smaller regions, which can then be regrouped.

Segger also achieves quick rigid fitting or docking of structures, by alignment of the structure with one or more segmented regions. The alignment is done by placing the structure so that its center of mass is the same as the center of mass of the region(s), and then either the principal axes are aligned, or the structure is rotated exhaustively. Each alignment is optimized by gradient ascent, finding a local optimum in the cross-correlation. All the CC-scores and fits can then be visually replayed by selecting them from a list. The cross-correlations scores are sorted from highest to lowest - when the highest CC score is significantly higheer, this gives higher confidence that the correct fit was found.

Software Package Details

Software Name: Segger

Software Licensing: GSL (open source)

Software URL: http://ncmi.bcm.edu/ncmi/software/segger/

Software Reference: See the webpage for detailed references.

Software Capabilities:

  • See the short description.

Software Description:

Segger is available as a plug-in to Chimera, and is included in version 1.5 and the latest daily builds.

It segments a map by first applying the watershed method and then grouping the resulting regions through scale-space filtering or smoothing using a Gaussian kernel. Most of the time regions corresponding to proteins are obtained.

The grouping process produces a hierarchy, which is leveraged in interactive modification of the results. Ungrouping breaks up a region into smaller regions, which can then be regrouped.

Segger also achieves quick rigid fitting or docking of structures, by alignment of the structure with one or more segmented regions. The alignment is done by placing the structure so that its center of mass is the same as the center of mass of the region(s), and then either the principal axes are aligned, or the structure is rotated exhaustively. Each alignment is optimized by gradient ascent, finding a local optimum in the cross-correlation. All the CC-scores and fits can then be visually replayed by selecting them from a list. The cross-correlations scores are sorted from highest to lowest - when the highest CC score is significantly higheer, this gives higher confidence that the correct fit was found.

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