CYANA Command: atoms set - Revision history

Dean: /* Description */

2019-11-20T15:44:11Z

Description

← Older revision		Revision as of 17:44, 20 November 2019
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	:;rho :Used to set the rho parameter of selected atoms for eNOE calculations.		:;rho :Used to set the rho parameter of selected atoms for eNOE calculations.
	:;tauc :Used to set the tauc parameter of selected atoms for eNOE calculations.		:;tauc :Used to set the tauc parameter of selected atoms for eNOE calculations.
	;:occupancy : Used to set the occupancy parameter of selected atoms for writing multi-state structure files.		:;occupancy : Used to set the occupancy parameter of selected atoms for writing multi-state structure files.
	:;undefined :The coordinates of the selected atoms in the current structure are set as “undefined”, as if they would not have been read from an input coordinate file. With the additional option '''all''', the coordinates of the selected atoms are set as “undefined” also in all selected structures.		:;undefined :The coordinates of the selected atoms in the current structure are set as “undefined”, as if they would not have been read from an input coordinate file. With the additional option '''all''', the coordinates of the selected atoms are set as “undefined” also in all selected structures.

	Optionally, the command can be applied only to a ''random'' fraction of all selected atoms.		Optionally, the command can be applied only to a ''random'' fraction of all selected atoms.

Dean: /* Description */

2019-11-20T15:43:44Z

Description

← Older revision		Revision as of 17:43, 20 November 2019
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	:;rho :Used to set the rho parameter of selected atoms for eNOE calculations.		:;rho :Used to set the rho parameter of selected atoms for eNOE calculations.
	:;tauc :Used to set the tauc parameter of selected atoms for eNOE calculations.		:;tauc :Used to set the tauc parameter of selected atoms for eNOE calculations.
			;:occupancy : Used to set the occupancy parameter of selected atoms for writing multi-state structure files.
	:;undefined :The coordinates of the selected atoms in the current structure are set as “undefined”, as if they would not have been read from an input coordinate file. With the additional option '''all''', the coordinates of the selected atoms are set as “undefined” also in all selected structures.		:;undefined :The coordinates of the selected atoms in the current structure are set as “undefined”, as if they would not have been read from an input coordinate file. With the additional option '''all''', the coordinates of the selected atoms are set as “undefined” also in all selected structures.

	Optionally, the command can be applied only to a ''random'' fraction of all selected atoms.		Optionally, the command can be applied only to a ''random'' fraction of all selected atoms.

Dean: /* Parameters */

2019-11-20T15:42:31Z

Parameters

← Older revision		Revision as of 17:42, 20 November 2019
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	;rho=''real'': (default: ''none'')		;rho=''real'': (default: ''none'')
	;tauc=''real'': (default: ''none'')		;tauc=''real'': (default: ''none'')
			;occupancy=''real'': (default: ''none'')
	; undefined		; undefined
	; all		; all

Dean: /* Description */

2019-11-20T15:23:14Z

Description

← Older revision		Revision as of 17:23, 20 November 2019
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	:;protlev :Used to set the protlev parameter of selected atoms for eNOE calculations. The '''protlev''' parameter is be used to account for D2O exchange of amide atoms in solution, i.e. protlev=0.97 for D2O exchange in a buffer solution containing 3% D2O. For spin diffusion calculations using the TSS approach, the protlev parameter is used to account for versatile labeling patterns, such as used in methyl labeling, see * [[CYANA Command: enoe spindiff \|enoe spindiff]]		:;protlev :Used to set the protlev parameter of selected atoms for eNOE calculations. The '''protlev''' parameter is be used to account for D2O exchange of amide atoms in solution, i.e. protlev=0.97 for D2O exchange in a buffer solution containing 3% D2O. For spin diffusion calculations using the TSS approach, the protlev parameter is used to account for versatile labeling patterns, such as used in methyl labeling, see * [[CYANA Command: enoe spindiff \|enoe spindiff]]
	:;rho :Used to set the rho parameter of selected atoms for eNOE calculations.		:;rho :Used to set the rho parameter of selected atoms for eNOE calculations.
			:;tauc :Used to set the tauc parameter of selected atoms for eNOE calculations.
	:;undefined :The coordinates of the selected atoms in the current structure are set as “undefined”, as if they would not have been read from an input coordinate file. With the additional option '''all''', the coordinates of the selected atoms are set as “undefined” also in all selected structures.		:;undefined :The coordinates of the selected atoms in the current structure are set as “undefined”, as if they would not have been read from an input coordinate file. With the additional option '''all''', the coordinates of the selected atoms are set as “undefined” also in all selected structures.

	Optionally, the command can be applied only to a ''random'' fraction of all selected atoms.		Optionally, the command can be applied only to a ''random'' fraction of all selected atoms.

Dean: /* Parameters */

2019-11-20T15:22:38Z

Parameters

← Older revision		Revision as of 17:22, 20 November 2019
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	; protlev=''real'': (default: ''none'')		; protlev=''real'': (default: ''none'')
	;rho=''real'': (default: ''none'')		;rho=''real'': (default: ''none'')
			;tauc=''real'': (default: ''none'')
	; undefined		; undefined
	; all		; all

Dean: /* Description */

2019-11-20T15:19:37Z

Description

← Older revision		Revision as of 17:19, 20 November 2019
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	:;tolerance :Chemical shift uncertainty (in ppm).		:;tolerance :Chemical shift uncertainty (in ppm).
	:;residue :External residue number. The external residue number is changed for all residues for which at least one atom is selected.		:;residue :External residue number. The external residue number is changed for all residues for which at least one atom is selected.
	:;protlev:Used to set the protlev parameter of selected atoms for eNOE calculations. The '''protlev''' parameter is be used to account for D2O exchange of amide atoms in solution, i.e. protlev=0.97 for D2O exchange in a buffer solution containing 3% D2O. For spin diffusion calculations using the TSS approach, the protlev parameter is used to account for versatile labeling patterns, such as used in methyl labeling, see * [[CYANA Command: enoe spindiff \|enoe spindiff]]		:;protlev :Used to set the protlev parameter of selected atoms for eNOE calculations. The '''protlev''' parameter is be used to account for D2O exchange of amide atoms in solution, i.e. protlev=0.97 for D2O exchange in a buffer solution containing 3% D2O. For spin diffusion calculations using the TSS approach, the protlev parameter is used to account for versatile labeling patterns, such as used in methyl labeling, see * [[CYANA Command: enoe spindiff \|enoe spindiff]]
			:;rho :Used to set the rho parameter of selected atoms for eNOE calculations.
	:;undefined :The coordinates of the selected atoms in the current structure are set as “undefined”, as if they would not have been read from an input coordinate file. With the additional option '''all''', the coordinates of the selected atoms are set as “undefined” also in all selected structures.		:;undefined :The coordinates of the selected atoms in the current structure are set as “undefined”, as if they would not have been read from an input coordinate file. With the additional option '''all''', the coordinates of the selected atoms are set as “undefined” also in all selected structures.

	Optionally, the command can be applied only to a ''random'' fraction of all selected atoms.		Optionally, the command can be applied only to a ''random'' fraction of all selected atoms.

Dean: /* Parameters */

2019-11-20T15:18:38Z

Parameters

← Older revision		Revision as of 17:18, 20 November 2019
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	; random=''real'': (default: 1.0)		; random=''real'': (default: 1.0)
	; protlev=''real'': (default: ''none'')		; protlev=''real'': (default: ''none'')
			;rho=''real'': (default: ''none'')
	; undefined		; undefined
	; all		; all

Dean: /* Description */

2019-11-20T15:16:42Z

Description

← Older revision		Revision as of 17:16, 20 November 2019
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	:;tolerance :Chemical shift uncertainty (in ppm).		:;tolerance :Chemical shift uncertainty (in ppm).
	:;residue :External residue number. The external residue number is changed for all residues for which at least one atom is selected.		:;residue :External residue number. The external residue number is changed for all residues for which at least one atom is selected.
	::;protlev:Used to set the protlev parameter of selected atoms for eNOE calculations. The '''protlev''' parameter is be used to account for D2O exchange of amide atoms in solution, i.e. protlev=0.97 for D2O exchange in a buffer solution containing 3% D2O. For spin diffusion calculations using the TSS approach, the protlev parameter is used to account for versatile labeling patterns, such as used in methyl labeling, see * [[CYANA Command: enoe spindiff \|enoe spindiff]]		:;protlev:Used to set the protlev parameter of selected atoms for eNOE calculations. The '''protlev''' parameter is be used to account for D2O exchange of amide atoms in solution, i.e. protlev=0.97 for D2O exchange in a buffer solution containing 3% D2O. For spin diffusion calculations using the TSS approach, the protlev parameter is used to account for versatile labeling patterns, such as used in methyl labeling, see * [[CYANA Command: enoe spindiff \|enoe spindiff]]
	:;undefined :The coordinates of the selected atoms in the current structure are set as “undefined”, as if they would not have been read from an input coordinate file. With the additional option '''all''', the coordinates of the selected atoms are set as “undefined” also in all selected structures.		:;undefined :The coordinates of the selected atoms in the current structure are set as “undefined”, as if they would not have been read from an input coordinate file. With the additional option '''all''', the coordinates of the selected atoms are set as “undefined” also in all selected structures.

	Optionally, the command can be applied only to a ''random'' fraction of all selected atoms.		Optionally, the command can be applied only to a ''random'' fraction of all selected atoms.

Dean: /* Description */

2019-11-20T15:16:24Z

Description

← Older revision		Revision as of 17:16, 20 November 2019
Line 24:		Line 24:
	:;tolerance :Chemical shift uncertainty (in ppm).		:;tolerance :Chemical shift uncertainty (in ppm).
	:;residue :External residue number. The external residue number is changed for all residues for which at least one atom is selected.		:;residue :External residue number. The external residue number is changed for all residues for which at least one atom is selected.
			::;protlev:Used to set the protlev parameter of selected atoms for eNOE calculations. The '''protlev''' parameter is be used to account for D2O exchange of amide atoms in solution, i.e. protlev=0.97 for D2O exchange in a buffer solution containing 3% D2O. For spin diffusion calculations using the TSS approach, the protlev parameter is used to account for versatile labeling patterns, such as used in methyl labeling, see * [[CYANA Command: enoe spindiff \|enoe spindiff]]
	:;undefined :The coordinates of the selected atoms in the current structure are set as “undefined”, as if they would not have been read from an input coordinate file. With the additional option '''all''', the coordinates of the selected atoms are set as “undefined” also in all selected structures.		:;undefined :The coordinates of the selected atoms in the current structure are set as “undefined”, as if they would not have been read from an input coordinate file. With the additional option '''all''', the coordinates of the selected atoms are set as “undefined” also in all selected structures.

	Optionally, the command can be applied only to a ''random'' fraction of all selected atoms.		Optionally, the command can be applied only to a ''random'' fraction of all selected atoms.

Dean: /* Description */

2019-11-20T15:15:08Z

Description

← Older revision		Revision as of 17:15, 20 November 2019
Line 24:		Line 24:
	:;tolerance :Chemical shift uncertainty (in ppm).		:;tolerance :Chemical shift uncertainty (in ppm).
	:;residue :External residue number. The external residue number is changed for all residues for which at least one atom is selected.		:;residue :External residue number. The external residue number is changed for all residues for which at least one atom is selected.

	:;undefined :The coordinates of the selected atoms in the current structure are set as “undefined”, as if they would not have been read from an input coordinate file. With the additional option '''all''', the coordinates of the selected atoms are set as “undefined” also in all selected structures.		:;undefined :The coordinates of the selected atoms in the current structure are set as “undefined”, as if they would not have been read from an input coordinate file. With the additional option '''all''', the coordinates of the selected atoms are set as “undefined” also in all selected structures.

	Optionally, the command can be applied only to a ''random'' fraction of all selected atoms.		Optionally, the command can be applied only to a ''random'' fraction of all selected atoms.