Structure calculation with automated NOESY assignment - Revision history

Guentert at 14:27, 28 July 2019

2019-07-28T14:27:31Z

← Older revision		Revision as of 16:27, 28 July 2019
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	[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]		[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]
	Seven cycles of combined automated NOESY assignment and structure calculation, followed by a final structure calculation, are performed by the [[CYANA Macro: noeassign\|noeassign]] macro, which uses the [[CYANA Command: assign\|assign]] to perform the NOESY assignment. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An [[CYANA Macro: overview\|overview]] table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.		Seven cycles of combined automated NOESY assignment and structure calculation, followed by a final structure calculation, are performed by the [[CYANA Macro: noeassign\|noeassign]] macro, which uses the [[CYANA Command: assign\|assign]] command to perform the NOESY assignment. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An [[CYANA Macro: overview\|overview]] table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.

	An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable\|'''cyanatable''']] (at the Unix prompt) during or after the completion of the calculation.		An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable\|'''cyanatable''']] (at the Unix prompt) during or after the completion of the calculation.

Guentert at 14:04, 28 July 2019

2019-07-28T14:04:31Z

← Older revision		Revision as of 16:04, 28 July 2019
Line 26:		Line 26:

	[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]		[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]
	Seven cycles of combined automated NOESY assignment and structure calculation ~~are performed~~, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An [[CYANA Macro: overview\|overview]] table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.		Seven cycles of combined automated NOESY assignment and structure calculation, followed by a final structure calculation, are performed by the [[CYANA Macro: noeassign\|noeassign]] macro, which uses the [[CYANA Command: assign\|assign]] to perform the NOESY assignment. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An [[CYANA Macro: overview\|overview]] table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.

	An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable\|'''cyanatable''']] (at the Unix prompt) during or after the completion of the calculation.		An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable\|'''cyanatable''']] (at the Unix prompt) during or after the completion of the calculation.

Guentert at 13:59, 28 July 2019

2019-07-28T13:59:49Z

← Older revision		Revision as of 15:59, 28 July 2019
Line 24:		Line 24:

	First several variables are set: The variable '''peaks''' gives the names of the input peak lists, separated by commas without intervening blanks. The variable '''prot''' gives the name(s) of the input chemical shift list(s). If a single name is given as in the example, it specifies that a single chemical shift list file with this name will be used for all peak lists. Alternatively, it is possible to specify a separate chemical shift list for each peak list as a comma-separated list of file names. The variable '''restraints''' specifies the names of input files with additional conformational restraints that will be used together with the upper distance bounds that will be derived from the NOESY peaks. If there are several file names, they must be separated by commas without intervening blanks. The variable [[tolerance]] specifies the tolerances for the matching of chemical shifts. It is used for a consistency check of the peaks that have assignments in the input peak lists, and for the automated NOESY cross peak assignment. The calibration constants for the peak lists can be given by the variable '''calibration''' as a comma-separated list of values in the order of the peak list names given by the variable '''peaks'''. If the variable '''calibration''' is not given, the calibration parameters are determined automatically such that the median of the upper distance limits for each peak list equals the value of the variable '''calibration_dref'''. The variable '''calibration_dref''' can have a single value that applies to all peak lists, or separate values for each peak list. This variable is not used when the calibration constants are given explicitly by the variable '''calibration_constant'''.		First several variables are set: The variable '''peaks''' gives the names of the input peak lists, separated by commas without intervening blanks. The variable '''prot''' gives the name(s) of the input chemical shift list(s). If a single name is given as in the example, it specifies that a single chemical shift list file with this name will be used for all peak lists. Alternatively, it is possible to specify a separate chemical shift list for each peak list as a comma-separated list of file names. The variable '''restraints''' specifies the names of input files with additional conformational restraints that will be used together with the upper distance bounds that will be derived from the NOESY peaks. If there are several file names, they must be separated by commas without intervening blanks. The variable [[tolerance]] specifies the tolerances for the matching of chemical shifts. It is used for a consistency check of the peaks that have assignments in the input peak lists, and for the automated NOESY cross peak assignment. The calibration constants for the peak lists can be given by the variable '''calibration''' as a comma-separated list of values in the order of the peak list names given by the variable '''peaks'''. If the variable '''calibration''' is not given, the calibration parameters are determined automatically such that the median of the upper distance limits for each peak list equals the value of the variable '''calibration_dref'''. The variable '''calibration_dref''' can have a single value that applies to all peak lists, or separate values for each peak list. This variable is not used when the calibration constants are given explicitly by the variable '''calibration_constant'''.



	[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]		[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]

Guentert at 13:51, 28 July 2019

2019-07-28T13:51:35Z

← Older revision		Revision as of 15:51, 28 July 2019
Line 24:		Line 24:

	First several variables are set: The variable '''peaks''' gives the names of the input peak lists, separated by commas without intervening blanks. The variable '''prot''' gives the name(s) of the input chemical shift list(s). If a single name is given as in the example, it specifies that a single chemical shift list file with this name will be used for all peak lists. Alternatively, it is possible to specify a separate chemical shift list for each peak list as a comma-separated list of file names. The variable '''restraints''' specifies the names of input files with additional conformational restraints that will be used together with the upper distance bounds that will be derived from the NOESY peaks. If there are several file names, they must be separated by commas without intervening blanks. The variable [[tolerance]] specifies the tolerances for the matching of chemical shifts. It is used for a consistency check of the peaks that have assignments in the input peak lists, and for the automated NOESY cross peak assignment. The calibration constants for the peak lists can be given by the variable '''calibration''' as a comma-separated list of values in the order of the peak list names given by the variable '''peaks'''. If the variable '''calibration''' is not given, the calibration parameters are determined automatically such that the median of the upper distance limits for each peak list equals the value of the variable '''calibration_dref'''. The variable '''calibration_dref''' can have a single value that applies to all peak lists, or separate values for each peak list. This variable is not used when the calibration constants are given explicitly by the variable '''calibration_constant'''.		First several variables are set: The variable '''peaks''' gives the names of the input peak lists, separated by commas without intervening blanks. The variable '''prot''' gives the name(s) of the input chemical shift list(s). If a single name is given as in the example, it specifies that a single chemical shift list file with this name will be used for all peak lists. Alternatively, it is possible to specify a separate chemical shift list for each peak list as a comma-separated list of file names. The variable '''restraints''' specifies the names of input files with additional conformational restraints that will be used together with the upper distance bounds that will be derived from the NOESY peaks. If there are several file names, they must be separated by commas without intervening blanks. The variable [[tolerance]] specifies the tolerances for the matching of chemical shifts. It is used for a consistency check of the peaks that have assignments in the input peak lists, and for the automated NOESY cross peak assignment. The calibration constants for the peak lists can be given by the variable '''calibration''' as a comma-separated list of values in the order of the peak list names given by the variable '''peaks'''. If the variable '''calibration''' is not given, the calibration parameters are determined automatically such that the median of the upper distance limits for each peak list equals the value of the variable '''calibration_dref'''. The variable '''calibration_dref''' can have a single value that applies to all peak lists, or separate values for each peak list. This variable is not used when the calibration constants are given explicitly by the variable '''calibration_constant'''.



	[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]		[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]

Guentert at 13:27, 28 July 2019

2019-07-28T13:27:24Z

← Older revision		Revision as of 15:27, 28 July 2019
Line 1:		Line 1:
	This calculation shows how to calculate a structure from previously unassigned NOESY peak lists. The input data are in the subdirectory ~~‘auto’~~ of the ~~[[Media:Cyana-3.0-demo.zip\|demo data zip archive]]~~:		This calculation shows how to calculate a structure from previously unassigned NOESY peak lists. The input data are in the subdirectory ‘demo/auto’ of the CYANA software package:

	;demo.seq:amino acid sequence		;demo.seq:amino acid sequence
Line 7:		Line 7:
	;demo.prot:<sup>1</sup>H, <sup>13</sup>C, and <sup>15</sup>N chemical shift list		;demo.prot:<sup>1</sup>H, <sup>13</sup>C, and <sup>15</sup>N chemical shift list
	;demo.aco:dihedral angle restraints		;demo.aco:dihedral angle restraints
	;~~init.cya:initialization macro~~		;CALC.cya:macro for the structure calculation
	~~;AUTO~~.cya:macro for the structure calculation


	Combined automated NOESY cross peak assignment and structure calculation are performed with the macro file '''~~AUTO~~.cya''':		Combined automated NOESY cross peak assignment and structure calculation are performed with the macro file '''CALC.cya''':

	peaks := c13.peaks,n15.peaks,aro.peaks # NOESY peak lists in XEASY ~~format~~		peaks := c13.peaks, n15.peaks, aro.peaks # NOESY peak lists in XEASY format
	~~#peaks := c13.xpk,n15.xpk,aro.xpk # alternative peak lists in NMRView~~ format		prot := demo.prot # names of chemical shift list(s)
	prot := demo.prot # names of chemical shift ~~lists~~		restraints := demo.aco # additional (non-NOE) restraints
	restraints := demo.aco # additional (non-NOE) restraints		tolerance := 0.04, 0.03, 0.45 # shift tolerances: H, H', C/N', C/N
	tolerance := 0.~~040~~,0.~~030~~,0.45 # shift tolerances: H, H', C/N', C/N		#calibration_constant:=6.7E5,8.2E5,8.0E4 # calibration constants, automatic if empty
	#calibration_constant:=6.7E5,8.2E5,8.0E4 # calibration constants, automatic if empty		structures := 100,20 # number of initial, final structures
	structures := 100,20 # number of initial, final structures		steps := 10000 # number of torsion angle dynamics steps
	steps := 10000 # number of torsion angle dynamics steps		randomseed := 434726 # random number generator seed
	randomseed := 434726 # random number generator seed

	noeassign peaks=$peaks prot=$prot autoaco ~~# perform NOESY assignment/structure calculation~~		noeassign peaks="$peaks" prot="$prot" autoaco

	First several variables are set: The variable '''peaks''' gives the names of the input peak lists, separated by commas without intervening blanks. The variable '''prot''' gives the name(s) of the input chemical shift list(s). If a single name is given as in the example, it specifies that a single chemical shift list file with this name will be used for all peak lists. Alternatively, it is possible to specify a separate chemical shift list for each peak list as a comma-separated list of file names. The variable '''restraints''' specifies the names of input files with additional conformational restraints that will be used together with the upper distance bounds that will be derived from the NOESY peaks. If there are several file names, they must be separated by commas without intervening blanks. The variable [[tolerance]] specifies the tolerances for the matching of chemical shifts. It is used for a consistency check of the peaks that have assignments in the input peak lists, and for the automated NOESY cross peak assignment. The calibration constants for the peak lists can be given by the variable '''calibration''' as a comma-separated list of values in the order of the peak list names given by the variable '''peaks'''. If the variable '''calibration''' is not given, the calibration parameters are determined automatically such that the median of the upper distance limits for each peak list equals the value of the variable '''calibration_dref'''. The variable '''calibration_dref''' can have a single value that applies to all peak lists, or separate values for each peak list. This variable is not used when the calibration constants are given explicitly by the variable '''calibration_constant'''.		First several variables are set: The variable '''peaks''' gives the names of the input peak lists, separated by commas without intervening blanks. The variable '''prot''' gives the name(s) of the input chemical shift list(s). If a single name is given as in the example, it specifies that a single chemical shift list file with this name will be used for all peak lists. Alternatively, it is possible to specify a separate chemical shift list for each peak list as a comma-separated list of file names. The variable '''restraints''' specifies the names of input files with additional conformational restraints that will be used together with the upper distance bounds that will be derived from the NOESY peaks. If there are several file names, they must be separated by commas without intervening blanks. The variable [[tolerance]] specifies the tolerances for the matching of chemical shifts. It is used for a consistency check of the peaks that have assignments in the input peak lists, and for the automated NOESY cross peak assignment. The calibration constants for the peak lists can be given by the variable '''calibration''' as a comma-separated list of values in the order of the peak list names given by the variable '''peaks'''. If the variable '''calibration''' is not given, the calibration parameters are determined automatically such that the median of the upper distance limits for each peak list equals the value of the variable '''calibration_dref'''. The variable '''calibration_dref''' can have a single value that applies to all peak lists, or separate values for each peak list. This variable is not used when the calibration constants are given explicitly by the variable '''calibration_constant'''.

Guentert at 13:57, 31 July 2011

2011-07-31T13:57:30Z

← Older revision		Revision as of 15:57, 31 July 2011
Line 28:		Line 28:

	[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]		[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]
	Seven cycles of combined automated NOESY assignment and structure calculation are performed, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An overview table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.		Seven cycles of combined automated NOESY assignment and structure calculation are performed, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An [[CYANA Macro: overview\|overview]] table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.

	An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable\|'''cyanatable''']] (at the Unix prompt) during or after the completion of the calculation.		An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable\|'''cyanatable''']] (at the Unix prompt) during or after the completion of the calculation.

Guentert at 21:47, 28 July 2009

2009-07-28T21:47:38Z

← Older revision		Revision as of 23:47, 28 July 2009
Line 30:		Line 30:
	Seven cycles of combined automated NOESY assignment and structure calculation are performed, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An overview table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.		Seven cycles of combined automated NOESY assignment and structure calculation are performed, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An overview table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.

	An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable\|'''cyanatable''']] during or after the completion of the calculation.		An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable\|'''cyanatable''']] (at the Unix prompt) during or after the completion of the calculation.

Guentert at 21:46, 28 July 2009

2009-07-28T21:46:40Z

← Older revision		Revision as of 23:46, 28 July 2009
Line 30:		Line 30:
	Seven cycles of combined automated NOESY assignment and structure calculation are performed, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An overview table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.		Seven cycles of combined automated NOESY assignment and structure calculation are performed, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An overview table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.

	An overview table of the complete calculation can be obtained with the command [[CYANA script: ~~cyanatabl~~\|'''cyanatable''']] during or after the completion of the calculation.		An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable\|'''cyanatable''']] during or after the completion of the calculation.

Guentert at 21:45, 28 July 2009

2009-07-28T21:45:05Z

← Older revision		Revision as of 23:45, 28 July 2009
Line 30:		Line 30:
	Seven cycles of combined automated NOESY assignment and structure calculation are performed, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An overview table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.		Seven cycles of combined automated NOESY assignment and structure calculation are performed, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An overview table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.

	An overview table of the complete calculation can be obtained with the command '''cyanatable''' during or after the completion of the calculation.		An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatabl\|'''cyanatable''']] during or after the completion of the calculation.

Guentert at 21:25, 28 July 2009

2009-07-28T21:25:10Z

← Older revision		Revision as of 23:25, 28 July 2009
Line 25:		Line 25:
	noeassign peaks=$peaks prot=$prot autoaco # perform NOESY assignment/structure calculation		noeassign peaks=$peaks prot=$prot autoaco # perform NOESY assignment/structure calculation

	First several variables are set: The variable '''peaks''' gives the names of the input peak lists, separated by commas without intervening blanks. The variable '''prot''' gives the name(s) of the input chemical shift list(s). If a single name is given as in the example, it specifies that a single chemical shift list file with this name will be used for all peak lists. Alternatively, it is possible to specify a separate chemical shift list for each peak list as a comma-separated list of file names. The variable '''restraints''' specifies the names of input files with additional conformational restraints that will be used together with the upper distance bounds that will be derived from the NOESY peaks. If there are several file names, they must be separated by commas without intervening blanks. The variable [[tolerance]] specifies the tolerances for the matching of chemical shifts~~, and~~ is used ~~only~~ for ~~the~~ consistency check. The calibration constants for the peak lists can be given by the variable '''calibration''' as a comma-separated list of values in the order of the peak list names given by the variable '''peaks'''. If the variable '''calibration''' is not given, the calibration parameters are determined automatically such that the median of the upper distance limits for each peak list equals the value of the variable '''~~dref~~'''. The variable '''~~dref~~''' can have a single value that applies to all peak lists, or separate values for each peak list. This variable is not used when the calibration constants are given explicitly by the variable '''calibration_constant'''.		First several variables are set: The variable '''peaks''' gives the names of the input peak lists, separated by commas without intervening blanks. The variable '''prot''' gives the name(s) of the input chemical shift list(s). If a single name is given as in the example, it specifies that a single chemical shift list file with this name will be used for all peak lists. Alternatively, it is possible to specify a separate chemical shift list for each peak list as a comma-separated list of file names. The variable '''restraints''' specifies the names of input files with additional conformational restraints that will be used together with the upper distance bounds that will be derived from the NOESY peaks. If there are several file names, they must be separated by commas without intervening blanks. The variable [[tolerance]] specifies the tolerances for the matching of chemical shifts. It is used for a consistency check of the peaks that have assignments in the input peak lists, and for the automated NOESY cross peak assignment. The calibration constants for the peak lists can be given by the variable '''calibration''' as a comma-separated list of values in the order of the peak list names given by the variable '''peaks'''. If the variable '''calibration''' is not given, the calibration parameters are determined automatically such that the median of the upper distance limits for each peak list equals the value of the variable '''calibration_dref'''. The variable '''calibration_dref''' can have a single value that applies to all peak lists, or separate values for each peak list. This variable is not used when the calibration constants are given explicitly by the variable '''calibration_constant'''.

	[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]		[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]
	~~Finally~~, ~~the sequence~~ and the ~~conformational restraints are read and~~ 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. ~~Finally, the~~ 20 conformers with the lowest final target function values are analyzed. An overview table of these 20 best conformers is saved in the file '''~~demo~~.ovw''', and their coordinates are written to the PDB file '''~~demo~~.pdb'''.		Seven cycles of combined automated NOESY assignment and structure calculation are performed, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An overview table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.

			An overview table of the complete calculation can be obtained with the command '''cyanatable''' during or after the completion of the calculation.

← Older revision		Revision as of 16:27, 28 July 2019
Line 26:		Line 26:

	[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]		[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]
	Seven cycles of combined automated NOESY assignment and structure calculation, followed by a final structure calculation, are performed by the [[CYANA Macro: noeassign\|noeassign]] macro, which uses the [[CYANA Command: assign\|assign]] to perform the NOESY assignment. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An [[CYANA Macro: overview\|overview]] table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.		Seven cycles of combined automated NOESY assignment and structure calculation, followed by a final structure calculation, are performed by the [[CYANA Macro: noeassign\|noeassign]] macro, which uses the [[CYANA Command: assign\|assign]] command to perform the NOESY assignment. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An [[CYANA Macro: overview\|overview]] table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.

	An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable\|'''cyanatable''']] (at the Unix prompt) during or after the completion of the calculation.		An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable\|'''cyanatable''']] (at the Unix prompt) during or after the completion of the calculation.

← Older revision		Revision as of 16:04, 28 July 2019
Line 26:		Line 26:

	[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]		[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]
	Seven cycles of combined automated NOESY assignment and structure calculation ~~are performed~~, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An [[CYANA Macro: overview\|overview]] table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.		Seven cycles of combined automated NOESY assignment and structure calculation, followed by a final structure calculation, are performed by the [[CYANA Macro: noeassign\|noeassign]] macro, which uses the [[CYANA Command: assign\|assign]] to perform the NOESY assignment. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An [[CYANA Macro: overview\|overview]] table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.

	An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable\|'''cyanatable''']] (at the Unix prompt) during or after the completion of the calculation.		An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable\|'''cyanatable''']] (at the Unix prompt) during or after the completion of the calculation.

← Older revision		Revision as of 15:57, 31 July 2011
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	[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]		[[Image:StructuresDemoManual.png\|thumb\|200px\|'''demo.pdb''']]
	Seven cycles of combined automated NOESY assignment and structure calculation are performed, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An overview table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.		Seven cycles of combined automated NOESY assignment and structure calculation are performed, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [[simulated annealing]] schedule with 10000 [[torsion angle dynamics]] steps per conformer. The 20 conformers with the lowest final target function values are analyzed. An [[CYANA Macro: overview\|overview]] table of these 20 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.

	An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable\|'''cyanatable''']] (at the Unix prompt) during or after the completion of the calculation.		An overview table of the complete calculation can be obtained with the command [[CYANA script: cyanatable\|'''cyanatable''']] (at the Unix prompt) during or after the completion of the calculation.