Residue library file - Revision history

Guentert at 07:11, 22 July 2014

2014-07-22T07:11:02Z

← Older revision		Revision as of 09:11, 22 July 2014
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	To avoid nomenclature confusion all atom types and residue entries of		To avoid nomenclature confusion all atom types and residue entries of
	the standard residue library file are listed in the following ~~(for compactness~~		the standard residue library file are listed in the following:
	~~two numbers that are not used by CYANA are not printed in the atom~~
	~~lines between the atom type and the x-coordinate)~~:

	ATOMTYPES 20 0.10		ATOMTYPES 20 0.10

Admin at 13:58, 25 August 2009

2009-08-25T13:58:56Z

← Older revision		Revision as of 15:58, 25 August 2009
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	* the atom type		* the atom type
	* the repulsive core radius that will be assigned to atoms of this type		* the repulsive core radius that will be assigned to atoms of this type
	* a code for hydrogen bond capabilities (1 for hydrogen atoms that can form hydrogen bonds, for hydrogen bond acceptors (e.g. oxygens), and 0 for atoms that cannot be involved in hydrogen bonds)		* a code for hydrogen bond capabilities (1 for hydrogen atoms that can form hydrogen bonds, -1 for hydrogen bond acceptors (e.g. oxygens), and 0 for atoms that cannot be involved in hydrogen bonds)
	* the order number of the chemical element (0 for pseudo atoms, 1 for hydrogen, 6 for carbon, 7 for nitrogen etc.)		* the order number of the chemical element (0 for pseudo atoms, 1 for hydrogen, 6 for carbon, 7 for nitrogen etc.)

Guentert at 14:14, 11 August 2009

2009-08-11T14:14:35Z

Guentert at 14:13, 11 August 2009

2009-08-11T14:13:11Z

Guentert at 14:12, 11 August 2009

2009-08-11T14:12:05Z

← Older revision		Revision as of 16:12, 11 August 2009
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	# the atom type (used to set the repulsive core radii)		# the atom type (used to set the repulsive core radii)
	# the x-, y- and z-coordinates in for an arbitrary conformation		# the x-, y- and z-coordinates in for an arbitrary conformation
	# four atom numbers indicating covalent connectivities (if there are less than four connectivities, the corresponding		# four atom numbers indicating covalent connectivities (if there are less than four connectivities, the corresponding numbers are set to 0)
	numbers are set to 0)
	# the atom number of the corresponding pseudo atom (or 0 if there is no corresponding pseudo atom).		# the atom number of the corresponding pseudo atom (or 0 if there is no corresponding pseudo atom).

Guentert at 14:11, 11 August 2009

2009-08-11T14:11:24Z

← Older revision		Revision as of 16:11, 11 August 2009
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	type declarations that will follow. The following lines contain atom type		type declarations that will follow. The following lines contain atom type
	declarations in the Fortran format (5X,A5,F10.2,2I5):		declarations in the Fortran format (5X,A5,F10.2,2I5):

	# the atom type		# the atom type
	# the repulsive core radius that will be assigned to atoms of this type		# the repulsive core radius that will be assigned to atoms of this type
	# a code for hydrogen bond capabilities (1 for hydrogen atoms that can form hydrogen		# a code for hydrogen bond capabilities (1 for hydrogen atoms that can form hydrogen bonds, for hydrogen bond acceptors (e.g. oxygens), and 0 for atoms that cannot be involved in hydrogen bonds)
	bonds, for hydrogen bond acceptors (e.g. oxygens), and 0 for atoms		# the order number of the chemical element (0 for pseudo atoms, 1 for hydrogen, 6 for carbon, 7 for nitrogen etc.).
	that cannot be involved in hydrogen bonds)
	# the order number of the chemical element (0 for pseudo atoms, 1 for hydrogen, 6 for carbon,
	7 for nitrogen etc.).

	The atom types entry must precede the residue entries.		The atom types entry must precede the residue entries.

	A residue entry starts with a header line with the Fortran format		A residue entry starts with a header line with the Fortran format
	(A10,A5,4I5) and containing the word RESIDUE, the residue name, the		(A10,A5,4I5) and containing
	~~numbers~~ of rotatable dihedral angle ~~and~~ atom declarations that will follow,
	~~respectively, and~~ the numbers of the first ~~and~~ last atom in the list of		# the word RESIDUE
	atom declarations that ~~belong~~ to the residue (not to the ~~preceding or~~ following		# the residue name
	~~one~~ in the polypeptide chain). The next lines contain dihedral angle		# the number of rotatable dihedral angle declarations that will follow
	declarations in the format (5X,A5,20X,5I5): the dihedral angle		# the number of atom declarations that will follow
	~~name,~~ the numbers of the four atoms that define the dihedral angle~~, and~~ the		# the numbers of the first atom in the list of atom declarations that belongs to the residue (not to the preceding residue in the polypeptide chain)
	number of the last atom that will be affected by a rotation of the dihedral		# the numbers of the last atom in the list of atom declarations that belongs to the residue (not to the following residue in the polypeptide chain).
	angle (for backbone dihedral angles this number is set to 0). Atom
	numbers correspond to the running numbers in the first column of the		The next lines contain dihedral angle declarations in the format (5X,A5,20X,5I5):

			# the dihedral angle name
			# the numbers of the four atoms that define the dihedral angle
			# the number of the last atom that will be affected by a rotation of the dihedral angle (for backbone dihedral angles this number is set to 0).

			Atom numbers correspond to the running numbers in the first column of the
	atom declarations. The atom declarations must be ordered such that the		atom declarations. The atom declarations must be ordered such that the
	set of atoms affected by a change of a dihedral angle consists of all atoms		set of atoms affected by a change of a dihedral angle consists of all atoms
	following the third atom in the dihedral angle definition up to the last		following the third atom in the dihedral angle definition up to the last
	atom (or the C-terminus for backbone dihedral angles) that is affected.		atom (or the C-terminus for backbone dihedral angles) that is affected.

	Finally, there are lines containing atom declarations: the format is		Finally, there are lines containing atom declarations: the format is
	(5X,2A5,15X,3F10.4,5I5), the data are the atom name, the atom type		(5X,2A5,15X,3F10.4,5I5), the data are
	(used to set the repulsive core radii), the x-, y- and z-coordinates in for		# the atom name
	an arbitrary conformation, four atom numbers indicating covalent connectivities		# the atom type (used to set the repulsive core radii)
	(if there are less than four connectivities, the corresponding		# the x-, y- and z-coordinates in for an arbitrary conformation
	numbers are set to 0) ~~and~~ the atom number of the corresponding pseudo		# four atom numbers indicating covalent connectivities (if there are less than four connectivities, the corresponding
	atom (or 0 if there is no corresponding pseudo atom).		numbers are set to 0)
	The nomenclature of atoms in amino acid residues ~~closely~~ follows the		# the atom number of the corresponding pseudo atom (or 0 if there is no corresponding pseudo atom).
	IUPAC recommendations~~. The only exception is the backbone amide~~
	~~proton which is called HN instead of H~~. In addition to real atoms the residue		The nomenclature of atoms in amino acid residues follows the
			IUPAC recommendations (Markley et al, 1998). In addition to real atoms the residue
	library may contain pseudo atoms identified by the atom type		library may contain pseudo atoms identified by the atom type
	PSEUD that are used in CYANA as dimensionless reference points for		PSEUD that are used in CYANA as dimensionless reference points for

Guentert at 14:06, 11 August 2009

2009-08-11T14:06:11Z

← Older revision		Revision as of 16:06, 11 August 2009
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	(A10,I5) containing the word ATOMTYPES and the number of atom		(A10,I5) containing the word ATOMTYPES and the number of atom
	type declarations that will follow. The following lines contain atom type		type declarations that will follow. The following lines contain atom type
	declarations in the Fortran format (5X,A5,F10.2,2I5): the atom type, the		declarations in the Fortran format (5X,A5,F10.2,2I5):
	repulsive core radius that will be assigned to atoms of this type, a code		# the atom type
	for hydrogen bond capabilities (1 for hydrogen atoms that can form hydrogen		# the repulsive core radius that will be assigned to atoms of this type
			# a code for hydrogen bond capabilities (1 for hydrogen atoms that can form hydrogen
	bonds, for hydrogen bond acceptors (e.g. oxygens), and 0 for atoms		bonds, for hydrogen bond acceptors (e.g. oxygens), and 0 for atoms
	that cannot be involved in hydrogen bonds)~~, and~~ the order number		that cannot be involved in hydrogen bonds)
	of the chemical element (0 for pseudo atoms, 1 for hydrogen, 6 for carbon,		# the order number of the chemical element (0 for pseudo atoms, 1 for hydrogen, 6 for carbon,
	7 for nitrogen etc.). The atom types entry must precede the residue		7 for nitrogen etc.).
	entries.
			The atom types entry must precede the residue entries.

	A residue entry starts with a header line with the Fortran format		A residue entry starts with a header line with the Fortran format

Guentert at 14:04, 11 August 2009

2009-08-11T14:04:38Z

Masayo at 12:38, 15 July 2009

2009-07-15T12:38:13Z

← Older revision		Revision as of 14:38, 15 July 2009
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	~~===Residue library===~~

	The residue library input file declares the atom types, the nomenclature,		The residue library input file declares the atom types, the nomenclature,
	the dihedral angle definitions, the covalent connectivities and the standard		the dihedral angle definitions, the covalent connectivities and the standard

Masayo at 12:36, 15 July 2009

2009-07-15T12:36:31Z

← Older revision		Revision as of 14:36, 15 July 2009
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	The residue library input file declares the atom types, the nomenclature,		The residue library input file declares the atom types, the nomenclature,
	the dihedral angle definitions, the covalent connectivities and the standard		the dihedral angle definitions, the covalent connectivities and the standard
	geometry. The standard library, ~~“dyana~~.lib”, uses the standard geometry		geometry. The standard library, “cyana.lib”, uses the standard geometry
	of the ECEPP/2 force field (Momany et al., 1975; Némethy et al.,		of the ECEPP/2 force field (Momany et al., 1975; Némethy et al.,
	1983) for all amino acid residue types. The covalent geometry of the nucleotides		1983) for all amino acid residue types. The covalent geometry of the nucleotides

← Older revision		Revision as of 16:14, 11 August 2009
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	* the repulsive core radius that will be assigned to atoms of this type		* the repulsive core radius that will be assigned to atoms of this type
	* a code for hydrogen bond capabilities (1 for hydrogen atoms that can form hydrogen bonds, for hydrogen bond acceptors (e.g. oxygens), and 0 for atoms that cannot be involved in hydrogen bonds)		* a code for hydrogen bond capabilities (1 for hydrogen atoms that can form hydrogen bonds, for hydrogen bond acceptors (e.g. oxygens), and 0 for atoms that cannot be involved in hydrogen bonds)
	* the order number of the chemical element (0 for pseudo atoms, 1 for hydrogen, 6 for carbon, 7 for nitrogen etc.).		* the order number of the chemical element (0 for pseudo atoms, 1 for hydrogen, 6 for carbon, 7 for nitrogen etc.)

	The atom types entry must precede the residue entries.		The atom types entry must precede the residue entries.
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	* the number of atom declarations that will follow		* the number of atom declarations that will follow
	* the numbers of the first atom in the list of atom declarations that belongs to the residue (not to the preceding residue in the polypeptide chain)		* the numbers of the first atom in the list of atom declarations that belongs to the residue (not to the preceding residue in the polypeptide chain)
	* the numbers of the last atom in the list of atom declarations that belongs to the residue (not to the following residue in the polypeptide chain).		* the numbers of the last atom in the list of atom declarations that belongs to the residue (not to the following residue in the polypeptide chain)

	The next lines contain dihedral angle declarations in the format (5X,A5,20X,5I5):		The next lines contain dihedral angle declarations in the format (5X,A5,20X,5I5):
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	* the x-, y- and z-coordinates in for an arbitrary conformation		* the x-, y- and z-coordinates in for an arbitrary conformation
	* four atom numbers indicating covalent connectivities (if there are less than four connectivities, the corresponding numbers are set to 0)		* four atom numbers indicating covalent connectivities (if there are less than four connectivities, the corresponding numbers are set to 0)
	* the atom number of the corresponding pseudo atom (or 0 if there is no corresponding pseudo atom).		* the atom number of the corresponding pseudo atom (or 0 if there is no corresponding pseudo atom)

	The nomenclature of atoms in amino acid residues follows the		The nomenclature of atoms in amino acid residues follows the

← Older revision		Revision as of 16:13, 11 August 2009
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	declarations in the Fortran format (5X,A5,F10.2,2I5):		declarations in the Fortran format (5X,A5,F10.2,2I5):

	# the atom type		* the atom type
	# the repulsive core radius that will be assigned to atoms of this type		* the repulsive core radius that will be assigned to atoms of this type
	# a code for hydrogen bond capabilities (1 for hydrogen atoms that can form hydrogen bonds, for hydrogen bond acceptors (e.g. oxygens), and 0 for atoms that cannot be involved in hydrogen bonds)		* a code for hydrogen bond capabilities (1 for hydrogen atoms that can form hydrogen bonds, for hydrogen bond acceptors (e.g. oxygens), and 0 for atoms that cannot be involved in hydrogen bonds)
	# the order number of the chemical element (0 for pseudo atoms, 1 for hydrogen, 6 for carbon, 7 for nitrogen etc.).		* the order number of the chemical element (0 for pseudo atoms, 1 for hydrogen, 6 for carbon, 7 for nitrogen etc.).

	The atom types entry must precede the residue entries.		The atom types entry must precede the residue entries.
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	(A10,A5,4I5) and containing		(A10,A5,4I5) and containing

	# the word RESIDUE		* the word RESIDUE
	# the residue name		* the residue name
	# the number of rotatable dihedral angle declarations that will follow		* the number of rotatable dihedral angle declarations that will follow
	# the number of atom declarations that will follow		* the number of atom declarations that will follow
	# the numbers of the first atom in the list of atom declarations that belongs to the residue (not to the preceding residue in the polypeptide chain)		* the numbers of the first atom in the list of atom declarations that belongs to the residue (not to the preceding residue in the polypeptide chain)
	# the numbers of the last atom in the list of atom declarations that belongs to the residue (not to the following residue in the polypeptide chain).		* the numbers of the last atom in the list of atom declarations that belongs to the residue (not to the following residue in the polypeptide chain).

	The next lines contain dihedral angle declarations in the format (5X,A5,20X,5I5):		The next lines contain dihedral angle declarations in the format (5X,A5,20X,5I5):

	# the dihedral angle name		* the dihedral angle name
	# the numbers of the four atoms that define the dihedral angle		* the numbers of the four atoms that define the dihedral angle
	# the number of the last atom that will be affected by a rotation of the dihedral angle (for backbone dihedral angles this number is set to 0).		* the number of the last atom that will be affected by a rotation of the dihedral angle (for backbone dihedral angles this number is set to 0).

	Atom numbers correspond to the running numbers in the first column of the		Atom numbers correspond to the running numbers in the first column of the
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	Finally, there are lines containing atom declarations: the format is		Finally, there are lines containing atom declarations: the format is
	(5X,2A5,15X,3F10.4,5I5), the data are		(5X,2A5,15X,3F10.4,5I5), the data are
	# the atom name		* the atom name
	# the atom type (used to set the repulsive core radii)		* the atom type (used to set the repulsive core radii)
	# the x-, y- and z-coordinates in for an arbitrary conformation		* the x-, y- and z-coordinates in for an arbitrary conformation
	# four atom numbers indicating covalent connectivities (if there are less than four connectivities, the corresponding numbers are set to 0)		* four atom numbers indicating covalent connectivities (if there are less than four connectivities, the corresponding numbers are set to 0)
	# the atom number of the corresponding pseudo atom (or 0 if there is no corresponding pseudo atom).		* the atom number of the corresponding pseudo atom (or 0 if there is no corresponding pseudo atom).

	The nomenclature of atoms in amino acid residues follows the		The nomenclature of atoms in amino acid residues follows the

← Older revision		Revision as of 16:04, 11 August 2009
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	only the entries marked with the keywords ATOMTYPES or RESIDUE		only the entries marked with the keywords ATOMTYPES or RESIDUE
	are considered.		are considered.

	The atom types entry starts with a header line with the Fortran format		The atom types entry starts with a header line with the Fortran format
	(A10,I5) containing the word ATOMTYPES and the number of atom		(A10,I5) containing the word ATOMTYPES and the number of atom
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	7 for nitrogen etc.). The atom types entry must precede the residue		7 for nitrogen etc.). The atom types entry must precede the residue
	entries.		entries.

	A residue entry starts with a header line with the Fortran format		A residue entry starts with a header line with the Fortran format
	(A10,A5,4I5) and containing the word RESIDUE, the residue name, the		(A10,A5,4I5) and containing the word RESIDUE, the residue name, the
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	one in the polypeptide chain). The next lines contain dihedral angle		one in the polypeptide chain). The next lines contain dihedral angle
	declarations in the format (5X,A5,20X,5I5): the dihedral angle		declarations in the format (5X,A5,20X,5I5): the dihedral angle
	name, the numbers of the four atoms that define the dihedral angle, and the number of the last atom that will be affected by a rotation of the dihedral		name, the numbers of the four atoms that define the dihedral angle, and the
			number of the last atom that will be affected by a rotation of the dihedral
	angle (for backbone dihedral angles this number is set to 0). Atom		angle (for backbone dihedral angles this number is set to 0). Atom
	numbers correspond to the running numbers in the first column of the		numbers correspond to the running numbers in the first column of the
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	PSEUD that are used in CYANA as dimensionless reference points for		PSEUD that are used in CYANA as dimensionless reference points for
	distance constraints.		distance constraints.

	To avoid nomenclature confusion all atom types and residue entries of		To avoid nomenclature confusion all atom types and residue entries of
	the standard residue library file are listed in the following (for compactness		the standard residue library file are listed in the following (for compactness