Homodimer structure calculation with automated NOESY assignment - Revision history

Guentert at 20:41, 25 November 2009

2009-11-25T20:41:13Z

← Older revision		Revision as of 22:41, 25 November 2009
Line 38:		Line 38:
	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''']]-->
	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''']] (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 16:39, 29 September 2009

2009-09-29T16:39:54Z

← Older revision		Revision as of 18:39, 29 September 2009
Line 10:		Line 10:
	;AUTO.cya:macro for the structure calculation		;AUTO.cya:macro for the structure calculation

	The presence of a homodimer is specified by additional commands in the initialization macro file, init.cya:		The presence of a homodimer is specified by additional commands in the initialization macro file, '''init.cya''':

	name:=demo		name:=demo
Line 16:		Line 16:
	read seq demo.seq		read seq demo.seq

	molecules define 1..49 101..149		molecules define 1..49 101..149 # Two monomers of residues 1-49 and 101-149, respectively
	molecule identity		molecule identity # Apply torsion angle difference restraints to keep the
	weight_ide=0.03		weight_ide=0.03 # structures of two monomers identical
	molecule symdist "CA 1..49" "CA 101..149"		molecule symdist "CA 1..49" "CA 101..149" # Apply distance difference restraints for symmetry-
	weight_sym=0.0025		weight_sym=0.0025 # related distances for symmetric relative orientation

	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 '''AUTO.cya''':

Guentert at 16:27, 29 September 2009

2009-09-29T16:27:35Z

← Older revision		Revision as of 18:27, 29 September 2009
Line 4:		Line 4:
	;c13.peaks:peak list from 3D <sup>13</sup>C-resolved NOESY spectrum		;c13.peaks:peak list from 3D <sup>13</sup>C-resolved NOESY spectrum
	;n15.peaks:peak list from 3D <sup>15</sup>N-resolved NOESY spectrum		;n15.peaks:peak list from 3D <sup>15</sup>N-resolved NOESY spectrum
	;inter.peaks:peak list with intermolecular peaks from a filtered 3D <sup>13</sup>C-resolved NOESY spectrum (Assignments will be restricted to intermolecular ones if the "XEASY color code" in column 4 of the peak list is set to 9. Similarly, assignments can be restricted to intramolecular ones if the XEASY color code is set to 8.)		;inter.peaks:peak list with intermolecular peaks from a filtered 3D <sup>13</sup>C-resolved NOESY spectrum (Assignments will be restricted to intermolecular ones if the "XEASY color code" in the fifth column of the peak list is set to 9. Similarly, assignments can be restricted to intramolecular ones if the XEASY color code is set to 8.)
	;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

Guentert at 16:26, 29 September 2009

2009-09-29T16:26:40Z

← Older revision		Revision as of 18:26, 29 September 2009
Line 4:		Line 4:
	;c13.peaks:peak list from 3D <sup>13</sup>C-resolved NOESY spectrum		;c13.peaks:peak list from 3D <sup>13</sup>C-resolved NOESY spectrum
	;n15.peaks:peak list from 3D <sup>15</sup>N-resolved NOESY spectrum		;n15.peaks:peak list from 3D <sup>15</sup>N-resolved NOESY spectrum
	;inter.peaks:peak list with intermolecular peaks from a filtered 3D <sup>13</sup>C-resolved NOESY spectrum		;inter.peaks:peak list with intermolecular peaks from a filtered 3D <sup>13</sup>C-resolved NOESY spectrum (Assignments will be restricted to intermolecular ones if the "XEASY color code" in column 4 of the peak list is set to 9. Similarly, assignments can be restricted to intramolecular ones if the XEASY color code is set to 8.)
	;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

Guentert at 16:22, 29 September 2009

2009-09-29T16:22:20Z

← Older revision		Revision as of 18:22, 29 September 2009
Line 15:		Line 15:
	cyanalib		cyanalib
	read seq demo.seq		read seq demo.seq

	molecules define 1..49 101..149		molecules define 1..49 101..149
	molecule identity		molecule identity

Guentert: Created page with 'This calculation shows how to calculate the structure of a homodimeric protein from previously unassigned NOESY peak lists. The input data are in the subdirectory ‘dimer’ of …'

2009-09-29T16:20:35Z

Created page with 'This calculation shows how to calculate the structure of a homodimeric protein from previously unassigned NOESY peak lists. The input data are in the subdirectory ‘dimer’ of …'

New page

This calculation shows how to calculate the structure of a homodimeric protein from previously unassigned NOESY peak lists. The input data are in the subdirectory ‘dimer’ of the [[Media:Cyana-3.0-demo.zip|demo data zip archive]]:

;demo.seq:amino acid sequence
;c13.peaks:peak list from 3D 13C-resolved NOESY spectrum
;n15.peaks:peak list from 3D 15N-resolved NOESY spectrum
;inter.peaks:peak list with intermolecular peaks from a filtered 3D 13C-resolved NOESY spectrum
;demo.prot:1H, 13C, and 15N chemical shift list
;demo.aco:dihedral angle restraints
;init.cya:initialization macro
;AUTO.cya:macro for the structure calculation

The presence of a homodimer is specified by additional commands in the initialization macro file, init.cya:

name:=demo
cyanalib
read seq demo.seq

molecules define 1..49 101..149
molecule identity
weight_ide=0.03
molecule symdist "CA 1..49" "CA 101..149"
weight_sym=0.0025

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

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 lists
restraints := demo.aco # additional (non-NOE) restraints
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
structures := 100,20 # number of initial, final structures
steps := 10000 # number of torsion angle dynamics steps
randomseed := 434726 # random number generator seed

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. 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''']]
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''']] (at the Unix prompt) during or after the completion of the calculation.