CYANA Command: structures secondary: Difference between revisions
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; structures=''integer'': (default: 1) | ; structures=''integer'': (default: 1) | ||
; mode=classic|normal|psipred|simple|ovw|sep: (default: normal) | ; mode=classic|normal|psipred|simple|ovw|sep: (default: normal) | ||
== Description == | |||
Computes the secondary structure using the DSSP algorithm (Kabsch & Sander, 1983), which is based exclusively on the detection of hydrogen bonds. If multiple structures are selected, the secondary structure is reported for the individual structures only if information level is set to '''full''' or higher. Otherwise only the consensus secondary structure is reported. The consensus secondary structure for a structure bundle is obtained by considering all hydrogen bonds that occur in a minimal number of ''structures'', as defined by the '''structures''' parameter. The default is to use all hydrogen bonds that are found in any structure. | Computes the secondary structure using the DSSP algorithm (Kabsch & Sander, 1983), which is based exclusively on the detection of hydrogen bonds. If multiple structures are selected, the secondary structure is reported for the individual structures only if information level is set to '''full''' or higher. Otherwise only the consensus secondary structure is reported. The consensus secondary structure for a structure bundle is obtained by considering all hydrogen bonds that occur in a minimal number of ''structures'', as defined by the '''structures''' parameter. The default is to use all hydrogen bonds that are found in any structure. | ||
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The following '''mode'''s are supported for the output of the results: | The following '''mode'''s are supported for the output of the results: | ||
; classic: Output exactly as in the DSSP publication (Kabsch & Sander, 1983) | |||
; normal: | |||
; psipred: | |||
; simple: | |||
; ovw: | |||
; seo: | |||
Revision as of 15:14, 31 July 2011
Parameters
- structures=integer
- (default: 1)
- mode=classic|normal|psipred|simple|ovw|sep
- (default: normal)
Description
Computes the secondary structure using the DSSP algorithm (Kabsch & Sander, 1983), which is based exclusively on the detection of hydrogen bonds. If multiple structures are selected, the secondary structure is reported for the individual structures only if information level is set to full or higher. Otherwise only the consensus secondary structure is reported. The consensus secondary structure for a structure bundle is obtained by considering all hydrogen bonds that occur in a minimal number of structures, as defined by the structures parameter. The default is to use all hydrogen bonds that are found in any structure.
The following modes are supported for the output of the results:
- classic
- Output exactly as in the DSSP publication (Kabsch & Sander, 1983)
- normal
- psipred
- simple
- ovw
- seo