CYANA Command: structures secondary - Revision history

Guentert at 13:53, 31 July 2011

2011-07-31T13:53:58Z

← Older revision		Revision as of 15:53, 31 July 2011
Line 13:		Line 13:
	; normal: Same as 'classic', except that in the summary line bends ('s') and turns ('t') are indicated with lower instead of upper case letters.		; normal: Same as 'classic', except that in the summary line bends ('s') and turns ('t') are indicated with lower instead of upper case letters.
	; psipred: Single-line output in the format of the program [http://bioinf.cs.ucl.ac.uk/psipred/ PsiPred]. Helices are indicated by 'H', β-strands by 'E', and all other residues are designated 'C'.		; psipred: Single-line output in the format of the program [http://bioinf.cs.ucl.ac.uk/psipred/ PsiPred]. Helices are indicated by 'H', β-strands by 'E', and all other residues are designated 'C'.
	;　~~simple~~: Output only information on helices and β-strands. In the summary line, these are designated '3' for 3<sub>10</sub>-helices, 'H' for α-helices, and 'B' for β-strands.		;simple: Output only information on helices and β-strands. In the summary line, these are designated '3' for 3<sub>10</sub>-helices, 'H' for α-helices, and 'B' for β-strands.
	; ovw: List the secondary structure elements, one per line.		; ovw: List the secondary structure elements, one per line.
	; seo: Similar output of the secondary structure elements one per line, separate for helices and β-sheets.		; seo: Similar output of the secondary structure elements one per line, separate for helices and β-sheets.

Guentert at 13:53, 31 July 2011

2011-07-31T13:53:37Z

← Older revision		Revision as of 15:53, 31 July 2011
Line 11:		Line 11:

	; classic: Output exactly as in the DSSP publication (Kabsch & Sander, 1983)		; classic: Output exactly as in the DSSP publication (Kabsch & Sander, 1983)
	; normal: Same as 'classic', except that in the summary line bends ('s') and turns ('t') are indicated with lower instead of upper case letters~~. This is the default~~.		; normal: Same as 'classic', except that in the summary line bends ('s') and turns ('t') are indicated with lower instead of upper case letters.
	; psipred: Single-line output in the format of the program [http://bioinf.cs.ucl.ac.uk/psipred/ PsiPred]. Helices are indicated by 'H', β-strands by 'E', and all other residues are designated 'C'.		; psipred: Single-line output in the format of the program [http://bioinf.cs.ucl.ac.uk/psipred/ PsiPred]. Helices are indicated by 'H', β-strands by 'E', and all other residues are designated 'C'.
	;　simple: Output only information on helices and β-strands. In the summary line, these are designated '3' for 3<sub>10</sub>-helices, 'H' for α-helices, and 'B' for β-strands.		;　simple: Output only information on helices and β-strands. In the summary line, these are designated '3' for 3<sub>10</sub>-helices, 'H' for α-helices, and 'B' for β-strands.
	; ovw: List the secondary structure elements, one per line.		; ovw: List the secondary structure elements, one per line.
	; seo: Similar output of the secondary structure elements one per line, separate for helices and β-sheets.		; seo: Similar output of the secondary structure elements one per line, separate for helices and β-sheets.

Guentert at 13:52, 31 July 2011

2011-07-31T13:52:52Z

← Older revision		Revision as of 15:52, 31 July 2011
Line 12:		Line 12:
	; classic: Output exactly as in the DSSP publication (Kabsch & Sander, 1983)		; classic: Output exactly as in the DSSP publication (Kabsch & Sander, 1983)
	; normal: Same as 'classic', except that in the summary line bends ('s') and turns ('t') are indicated with lower instead of upper case letters. This is the default.		; normal: Same as 'classic', except that in the summary line bends ('s') and turns ('t') are indicated with lower instead of upper case letters. This is the default.
	; psipred: Single-line output in the format ~~for~~ the program PsiPred (). Helices are indicated by 'H', beta-strands by 'E', and all other residues are designated 'C'.		; psipred: Single-line output in the format of the program [http://bioinf.cs.ucl.ac.uk/psipred/ PsiPred]. Helices are indicated by 'H', β-strands by 'E', and all other residues are designated 'C'.
	;　simple: Output only information on helices and beta-strands. In the summary line, these are designated '3' for 3<sub>10</sub>-helices, 'H' for alpha-helices, and 'B' for beta-strands.		;　simple: Output only information on helices and β-strands. In the summary line, these are designated '3' for 3<sub>10</sub>-helices, 'H' for α-helices, and 'B' for β-strands.
	; ovw:		; ovw: List the secondary structure elements, one per line.
	; seo:		; seo: Similar output of the secondary structure elements one per line, separate for helices and β-sheets.

Guentert at 13:37, 31 July 2011

2011-07-31T13:37:15Z

← Older revision		Revision as of 15:37, 31 July 2011
Line 11:		Line 11:

	; classic: Output exactly as in the DSSP publication (Kabsch & Sander, 1983)		; classic: Output exactly as in the DSSP publication (Kabsch & Sander, 1983)
	; normal:		; normal: Same as 'classic', except that in the summary line bends ('s') and turns ('t') are indicated with lower instead of upper case letters. This is the default.
	; psipred:		; psipred: Single-line output in the format for the program PsiPred (). Helices are indicated by 'H', beta-strands by 'E', and all other residues are designated 'C'.
	;　simple:		;　simple: Output only information on helices and beta-strands. In the summary line, these are designated '3' for 3<sub>10</sub>-helices, 'H' for alpha-helices, and 'B' for beta-strands.
	; ovw:		; ovw:
	; seo:		; seo:

Guentert at 13:14, 31 July 2011

2011-07-31T13:14:55Z

← Older revision		Revision as of 15:14, 31 July 2011
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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.
Line 8:		Line 10:
	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)		; classic: Output exactly as in the DSSP publication (Kabsch & Sander, 1983)
	;; normal:		; normal:
	;; psipred:		; psipred:
	;;　simple:		;　simple:
	;; ovw:		; ovw:
	;; seo:		; seo:

Guentert at 13:14, 31 July 2011

2011-07-31T13:14:13Z

← Older revision		Revision as of 15:14, 31 July 2011
Line 8:		Line 8:
	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)		;; classic: Output exactly as in the DSSP publication (Kabsch & Sander, 1983)
	; normal:		;; normal:
	; psipred:		;; psipred:
	;　simple:		;;　simple:
	; ovw:		;; ovw:
	; seo:		;; seo:

Guentert at 13:13, 31 July 2011

2011-07-31T13:13:45Z

New page

== Parameters ==

; structures=''integer'': (default: 1)
; mode=classic|normal|psipred|simple|ovw|sep: (default: normal)

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 '''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:

Admin: 1 revision

2009-01-29T11:26:57Z

1 revision

New page

== Parameters ==

; structures=''integer'': (default: 1)
; mode=classic|normal|simple: (default: normal)