Basic structure calculation starting from given restraints - Revision history

Guentert at 07:27, 28 July 2019

2019-07-28T07:27:33Z

← Older revision		Revision as of 09:27, 28 July 2019
Line 1:		Line 1:
	This calculation shows how to calculate a structure from previously assigned upper limits and dihedral angle restraints. The input data are in the subdirectory ~~‘basic’~~ of the ~~[[Media:Cyana-3.0-demo.zip\|demo data zip archive]]~~:		This calculation shows how to calculate a structure from previously assigned upper limits and dihedral angle restraints. The input data are in the 'demo/basic' subdirectory of the CYANA software package:

	;demo.seq:amino acid sequence		;demo.seq:amino acid sequence
	;demo.upl:upper distance limit restraints		;demo.upl:upper distance limit restraints
	;demo.aco:dihedral angle restraints		;demo.aco:dihedral angle restraints
	~~;init.cya:initialization macro~~
	;CALC.cya:macro for the structure calculation		;CALC.cya:macro for the structure calculation

			When CYANA is started, it automatically reads the standard amino acid library and the amino acid sequence of the protein (if multiple sequence files are in the current directory, the most recently modified one is read).
	When CYANA is started, it automatically ~~executes the commands in the initialization macro file '''init.cya''', which usually holds basic setup for the calculations, e.g., reading~~ the amino acid library and the amino acid sequence of the protein~~, and specifying general parameters such as the residue range for RMSD calculations. These commands could be put into the '''CALC.cya''' macro file~~ (~~or even given on~~ the ~~command line)~~, ~~but as they are rarely changed for a given project, it~~ is ~~convenient have them in the '''init.cya''' file:~~

	~~rmsdrange:=10-100 # define residue range for RMSD calculations~~
	~~cyanalib #~~ read ~~standard CYANA residue library~~
	~~read seq demo~~.~~seq # read amino acid sequence~~

	The actual structure calculation is performed by the commands in the macro file '''CALC.cya''':		The actual structure calculation is performed by the commands in the macro file '''CALC.cya''':

Guentert at 07:23, 28 July 2019

2019-07-28T07:23:21Z

← Older revision		Revision as of 09:23, 28 July 2019
Line 1:		Line 1:
	This calculation shows how to calculate a structure from previously assigned upper limits. The input data are in the subdirectory ‘basic’ of the [[Media:Cyana-3.0-demo.zip\|demo data zip archive]]:		This calculation shows how to calculate a structure from previously assigned upper limits and dihedral angle restraints. The input data are in the subdirectory ‘basic’ of the [[Media:Cyana-3.0-demo.zip\|demo data zip archive]]:

	;demo.seq:amino acid sequence		;demo.seq:amino acid sequence

Guentert at 13:57, 31 July 2011

2011-07-31T13:57:01Z

← Older revision		Revision as of 15:57, 31 July 2011
Line 24:		Line 24:

	[[Image:StructuresDemoBasic.png\|thumb\|200px\|'''demo.pdb''']]		[[Image:StructuresDemoBasic.png\|thumb\|200px\|'''demo.pdb''']]
	The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. The coordinates of these 10 best conformers are written to the PDB file '''demo.pdb''', and an overview table is saved in the file '''demo.ovw''':		The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. The coordinates of these 10 best conformers are written to the PDB file '''demo.pdb''', and an [[CYANA Macro: overview\|overview]] table is saved in the file '''demo.ovw''':

	Structural statistics:		Structural statistics:

Guentert at 13:46, 2 June 2009

2009-06-02T13:46:02Z

← Older revision		Revision as of 15:46, 2 June 2009
Line 19:		Line 19:
	read aco demo.aco # read dihedral angle restraints		read aco demo.aco # read dihedral angle restraints

	calc_all 50 steps=4000 # calculate conformers		calc_all 50 steps=4000 # calculate conformers

	overview demo.ovw structures=10 pdb # analyze and write best conformers		overview demo.ovw structures=10 pdb # analyze and write best conformers

Guentert at 13:26, 2 June 2009

2009-06-02T13:26:44Z

← Older revision		Revision as of 15:26, 2 June 2009
Line 23:		Line 23:
	overview demo.ovw structures=10 pdb # analyze and write best conformers		overview demo.ovw structures=10 pdb # analyze and write best conformers

	[[Image:StructuresDemoBasic.png\|thumb\|200px\|'''demo.pdb'''.]]		[[Image:StructuresDemoBasic.png\|thumb\|200px\|'''demo.pdb''']]
	The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. The coordinates of these 10 best conformers are written to the PDB file '''demo.pdb''', and an overview table is saved in the file '''demo.ovw''':		The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. The coordinates of these 10 best conformers are written to the PDB file '''demo.pdb''', and an overview table is saved in the file '''demo.ovw''':

Guentert at 13:23, 2 June 2009

2009-06-02T13:23:19Z

Guentert at 13:20, 2 June 2009

2009-06-02T13:20:45Z

← Older revision		Revision as of 15:20, 2 June 2009
Line 24:		Line 24:

	[[Image:StructuresDemoBasic.png\|thumb\|200px\|'''demo.pdb'''.]]		[[Image:StructuresDemoBasic.png\|thumb\|200px\|'''demo.pdb'''.]]
	The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. ~~An overview table~~ of these 10 best conformers ~~is saved in~~ the file '''demo.~~ovw~~''', and ~~their coordinates are written to~~ the ~~PDB~~ file '''demo.~~pdb~~'''.		The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. The coordinates of these 10 best conformers are written to the PDB file '''demo.pdb''', and an overview table is saved in the file '''demo.ovw''':

			Structural statistics:

			str target upper limits van der Waals torsion angles
			function # rms max # sum max # rms max
			1 1.56 1 0.0073 0.36 5 5.2 0.34 0 0.3460 3.19
			2 1.87 2 0.0084 0.36 5 6.1 0.33 0 0.3813 3.63
			3 1.92 2 0.0083 0.36 5 5.8 0.36 0 0.3491 3.29
			4 1.94 1 0.0082 0.36 6 6.4 0.34 0 0.3478 3.46
			5 2.02 2 0.0080 0.35 7 5.7 0.34 0 0.5790 4.35
			6 2.05 1 0.0082 0.35 8 6.0 0.34 0 0.5704 4.29
			7 2.12 2 0.0092 0.36 4 6.5 0.35 0 0.3629 3.47
			8 2.20 4 0.0105 0.36 5 7.2 0.31 0 0.3597 3.45
			9 2.24 2 0.0087 0.36 6 7.4 0.34 0 0.3843 3.47
			10 2.34 3 0.0119 0.61 5 6.6 0.35 0 0.3309 3.05

			Ave 2.03 2 0.0089 0.38 6 6.3 0.34 0 0.4011 3.56
			+/- 0.21 1 0.0013 0.08 1 0.7 0.01 0 0.0881 0.41
			Min 1.56 1 0.0073 0.35 4 5.2 0.31 0 0.3309 3.05
			Max 2.34 4 0.0119 0.61 8 7.4 0.36 0 0.5790 4.35
			Cut 0.20 0.20 5.00

			Constraints violated in 3 or more structures:
			# mean max. 1 5 10
			Upper HA ASP 68 - H ASN 69 3.28 4 0.11 0.29 +* ++ peak 1162
			Upper HB ILE 85 - H ASP 86 3.80 10 0.36 0.36 +++++++++* peak 803
			VdW N LEU 39 - CD1 LEU 39 3.05 10 0.23 0.24 ++++++++*+
			VdW N ILE 81 - CD PRO 82 3.05 10 0.26 0.28 ++*+++++++
			VdW N ILE 81 - HD2 PRO 82 2.45 10 0.34 0.36 ++*+++++++
			VdW CG2 ILE 81 - C ILE 81 2.90 6 0.20 0.22 ++ ++ *+
			VdW CB THR 91 - H GLN 92 2.55 7 0.22 0.27 ++++++ *
			VdW O THR 91 - CB GLN 92 2.90 3 0.15 0.20 * ++
			VdW HA VAL 107 - CD PRO 108 2.60 4 0.18 0.30 *+ + +
			2 violated distance restraints.
			7 violated van der Waals restraints.
			0 violated angle restraints.

			RMSDs for residues 10..100:
			Average backbone RMSD to mean : 0.52 +/- 0.09 A (0.40..0.72 A; 10 structures)
			Average heavy atom RMSD to mean : 1.04 +/- 0.06 A (0.96..1.17 A; 10 structures)

Guentert at 13:17, 2 June 2009

2009-06-02T13:17:03Z

← Older revision		Revision as of 15:17, 2 June 2009
Line 23:		Line 23:
	overview demo.ovw structures=10 pdb # analyze and write best conformers		overview demo.ovw structures=10 pdb # analyze and write best conformers

			[[Image:StructuresDemoBasic.png\|thumb\|200px\|'''demo.pdb'''.]]
	The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. An overview table of these 10 best conformers is saved in the file '''demo.ovw''', and their coordinates are written to the PDB file '''demo.pdb'''.		The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. An overview table of these 10 best conformers is saved in the file '''demo.ovw''', and their coordinates are written to the PDB file '''demo.pdb'''.

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

Guentert at 13:16, 2 June 2009

2009-06-02T13:16:39Z

← Older revision		Revision as of 15:16, 2 June 2009
Line 25:		Line 25:
	The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. An overview table of these 10 best conformers is saved in the file '''demo.ovw''', and their coordinates are written to the PDB file '''demo.pdb'''.		The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. An overview table of these 10 best conformers is saved in the file '''demo.ovw''', and their coordinates are written to the PDB file '''demo.pdb'''.

	[[Image:StructuresDemoBasic.png\|thumb\|200px\|~~Structures obtained in a basic structure calculation starting from given restraints~~]]		[[Image:StructuresDemoBasic.png\|thumb\|200px\|'''demo.pdb'''.]]

Guentert at 13:01, 2 June 2009

2009-06-02T13:01:16Z

← Older revision		Revision as of 15:01, 2 June 2009
Line 25:		Line 25:
	The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. An overview table of these 10 best conformers is saved in the file '''demo.ovw''', and their coordinates are written to the PDB file '''demo.pdb'''.		The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. An overview table of these 10 best conformers is saved in the file '''demo.ovw''', and their coordinates are written to the PDB file '''demo.pdb'''.

	[[Image:StructuresDemoBasic.png\|Structures obtained in a basic structure calculation starting from given restraints]]		[[Image:StructuresDemoBasic.png\|thumb\|200px\|Structures obtained in a basic structure calculation starting from given restraints]]

← Older revision		Revision as of 15:23, 2 June 2009
Line 10:		Line 10:
	When CYANA is started, it automatically executes the commands in the initialization macro file '''init.cya''', which usually holds basic setup for the calculations, e.g., reading the amino acid library and the amino acid sequence of the protein, and specifying general parameters such as the residue range for RMSD calculations. These commands could be put into the '''CALC.cya''' macro file (or even given on the command line), but as they are rarely changed for a given project, it is convenient have them in the '''init.cya''' file:		When CYANA is started, it automatically executes the commands in the initialization macro file '''init.cya''', which usually holds basic setup for the calculations, e.g., reading the amino acid library and the amino acid sequence of the protein, and specifying general parameters such as the residue range for RMSD calculations. These commands could be put into the '''CALC.cya''' macro file (or even given on the command line), but as they are rarely changed for a given project, it is convenient have them in the '''init.cya''' file:

	rmsdrange:=10-100 # define residue range for RMSD calculations		rmsdrange:=10-100 # define residue range for RMSD calculations
	cyanalib # read standard CYANA residue library		cyanalib # read standard CYANA residue library
	read seq demo.seq # read amino acid sequence		read seq demo.seq # read amino acid sequence

	The actual structure calculation is performed by the commands in the macro file '''CALC.cya''':		The actual structure calculation is performed by the commands in the macro file '''CALC.cya''':

	read upl demo.upl # read upper distance bounds		read upl demo.upl # read upper distance bounds
	read aco demo.aco # read dihedral angle restraints		read aco demo.aco # read dihedral angle restraints

	calc_all 50 steps=4000 # calculate conformers		calc_all 50 steps=4000 # calculate conformers

	overview demo.ovw structures=10 pdb # analyze and write best conformers		overview demo.ovw structures=10 pdb # analyze and write best conformers

	[[Image:StructuresDemoBasic.png\|thumb\|200px\|'''demo.pdb'''.]]		[[Image:StructuresDemoBasic.png\|thumb\|200px\|'''demo.pdb'''.]]
	The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. The coordinates of these 10 best conformers are written to the PDB file '''demo.pdb''', and an overview table is saved in the file '''demo.ovw''':		The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. The coordinates of these 10 best conformers are written to the PDB file '''demo.pdb''', and an overview table is saved in the file '''demo.ovw''':

	Structural statistics:		Structural statistics:

	str target upper limits van der Waals torsion angles		str target upper limits van der Waals torsion angles
	function # rms max # sum max # rms max		function # rms max # sum max # rms max
	1 1.56 1 0.0073 0.36 5 5.2 0.34 0 0.3460 3.19		1 1.56 1 0.0073 0.36 5 5.2 0.34 0 0.3460 3.19
	2 1.87 2 0.0084 0.36 5 6.1 0.33 0 0.3813 3.63		2 1.87 2 0.0084 0.36 5 6.1 0.33 0 0.3813 3.63
	3 1.92 2 0.0083 0.36 5 5.8 0.36 0 0.3491 3.29		3 1.92 2 0.0083 0.36 5 5.8 0.36 0 0.3491 3.29
	4 1.94 1 0.0082 0.36 6 6.4 0.34 0 0.3478 3.46		4 1.94 1 0.0082 0.36 6 6.4 0.34 0 0.3478 3.46
	5 2.02 2 0.0080 0.35 7 5.7 0.34 0 0.5790 4.35		5 2.02 2 0.0080 0.35 7 5.7 0.34 0 0.5790 4.35
	6 2.05 1 0.0082 0.35 8 6.0 0.34 0 0.5704 4.29		6 2.05 1 0.0082 0.35 8 6.0 0.34 0 0.5704 4.29
	7 2.12 2 0.0092 0.36 4 6.5 0.35 0 0.3629 3.47		7 2.12 2 0.0092 0.36 4 6.5 0.35 0 0.3629 3.47
	8 2.20 4 0.0105 0.36 5 7.2 0.31 0 0.3597 3.45		8 2.20 4 0.0105 0.36 5 7.2 0.31 0 0.3597 3.45
	9 2.24 2 0.0087 0.36 6 7.4 0.34 0 0.3843 3.47		9 2.24 2 0.0087 0.36 6 7.4 0.34 0 0.3843 3.47
	10 2.34 3 0.0119 0.61 5 6.6 0.35 0 0.3309 3.05		10 2.34 3 0.0119 0.61 5 6.6 0.35 0 0.3309 3.05

	Ave 2.03 2 0.0089 0.38 6 6.3 0.34 0 0.4011 3.56		Ave 2.03 2 0.0089 0.38 6 6.3 0.34 0 0.4011 3.56
	+/- 0.21 1 0.0013 0.08 1 0.7 0.01 0 0.0881 0.41		+/- 0.21 1 0.0013 0.08 1 0.7 0.01 0 0.0881 0.41
	Min 1.56 1 0.0073 0.35 4 5.2 0.31 0 0.3309 3.05		Min 1.56 1 0.0073 0.35 4 5.2 0.31 0 0.3309 3.05
	Max 2.34 4 0.0119 0.61 8 7.4 0.36 0 0.5790 4.35		Max 2.34 4 0.0119 0.61 8 7.4 0.36 0 0.5790 4.35
	Cut 0.20 0.20 5.00		Cut 0.20 0.20 5.00

	Constraints violated in 3 or more structures:		Constraints violated in 3 or more structures:
	# mean max. 1 5 10		# mean max. 1 5 10
	Upper HA ASP 68 - H ASN 69 3.28 4 0.11 0.29 +* ++ peak 1162		Upper HA ASP 68 - H ASN 69 3.28 4 0.11 0.29 +* ++ peak 1162
	Upper HB ILE 85 - H ASP 86 3.80 10 0.36 0.36 +++++++++* peak 803		Upper HB ILE 85 - H ASP 86 3.80 10 0.36 0.36 +++++++++* peak 803
	VdW N LEU 39 - CD1 LEU 39 3.05 10 0.23 0.24 ++++++++*+		VdW N LEU 39 - CD1 LEU 39 3.05 10 0.23 0.24 ++++++++*+
	VdW N ILE 81 - CD PRO 82 3.05 10 0.26 0.28 ++*+++++++		VdW N ILE 81 - CD PRO 82 3.05 10 0.26 0.28 ++*+++++++
	VdW N ILE 81 - HD2 PRO 82 2.45 10 0.34 0.36 ++*+++++++		VdW N ILE 81 - HD2 PRO 82 2.45 10 0.34 0.36 ++*+++++++
	VdW CG2 ILE 81 - C ILE 81 2.90 6 0.20 0.22 ++ ++ *+		VdW CG2 ILE 81 - C ILE 81 2.90 6 0.20 0.22 ++ ++ *+
	VdW CB THR 91 - H GLN 92 2.55 7 0.22 0.27 ++++++ *		VdW CB THR 91 - H GLN 92 2.55 7 0.22 0.27 ++++++ *
	VdW O THR 91 - CB GLN 92 2.90 3 0.15 0.20 * ++		VdW O THR 91 - CB GLN 92 2.90 3 0.15 0.20 * ++
	VdW HA VAL 107 - CD PRO 108 2.60 4 0.18 0.30 *+ + +		VdW HA VAL 107 - CD PRO 108 2.60 4 0.18 0.30 *+ + +
	2 violated distance restraints.		2 violated distance restraints.
	7 violated van der Waals restraints.		7 violated van der Waals restraints.
	0 violated angle restraints.		0 violated angle restraints.

	RMSDs for residues 10..100:		RMSDs for residues 10..100:
	Average backbone RMSD to mean : 0.52 +/- 0.09 A (0.40..0.72 A; 10 structures)		Average backbone RMSD to mean : 0.52 +/- 0.09 A (0.40..0.72 A; 10 structures)
	Average heavy atom RMSD to mean : 1.04 +/- 0.06 A (0.96..1.17 A; 10 structures)		Average heavy atom RMSD to mean : 1.04 +/- 0.06 A (0.96..1.17 A; 10 structures)