CYANA Macro: habas - Revision history

Miki: /* Description */

2010-01-12T15:35:46Z

Description

← Older revision		Revision as of 17:35, 12 January 2010
Line 11:		Line 11:
	Performs for all amino acid residues in the given ''range'' grid searches comprising the backbone dihedral angles φ, ψ and the given side chain ''angles''. To specify more than one side-chain angle, the names must be given, separated by blanks and enclosed in double quotes. If the cutoff value for the local, fragment-based target function, fmax, is positive, then all conformations with a local target function value below fmax will be considered as allowed. Otherwise, a conformation will be allowed if no single restraint violation exceeds the corresponding cutoff value defined by the variables [[CYANA Variables: soft_upl\|'''soft_upl''']], [[CYANA Variables: soft_lol\|'''soft_lol''']], etc. Unless the '''continue''' option is set, the allowed ranges of dihedral angles will be initialized to allow all possible angle values before the grid searches are started. This macro provides the functions of the former Habas program (Güntert et al., 1989). The results include dihedral angle restraints and, if possible, stereospecific assignments for the diastereotopic groups in the fragment.		Performs for all amino acid residues in the given ''range'' grid searches comprising the backbone dihedral angles φ, ψ and the given side chain ''angles''. To specify more than one side-chain angle, the names must be given, separated by blanks and enclosed in double quotes. If the cutoff value for the local, fragment-based target function, fmax, is positive, then all conformations with a local target function value below fmax will be considered as allowed. Otherwise, a conformation will be allowed if no single restraint violation exceeds the corresponding cutoff value defined by the variables [[CYANA Variables: soft_upl\|'''soft_upl''']], [[CYANA Variables: soft_lol\|'''soft_lol''']], etc. Unless the '''continue''' option is set, the allowed ranges of dihedral angles will be initialized to allow all possible angle values before the grid searches are started. This macro provides the functions of the former Habas program (Güntert et al., 1989). The results include dihedral angle restraints and, if possible, stereospecific assignments for the diastereotopic groups in the fragment.

	'''habas angles=”CHI1 CHI2*” tfcut=0.05''' Perform grid searches for all amino acid residues including the dihedral angles φ, ψ, χ<sup>1</sup> and χ<sup>2</sup>. Allow conformations with local target function values up to 0.05.		'''habas angles=”CHI1 CHI2*” tfcut=0.05''' Perform grid searches for all amino acid residues including the dihedral angles φ, ψ, χ<sup>1</sup> and χ<sup>2</sup>. Allow conformations with local target function values up to 0.05.

Miki: /* Description */

2010-01-12T15:30:00Z

Description

← Older revision		Revision as of 17:30, 12 January 2010
Line 9:		Line 9:
	== Description ==		== Description ==

	Performs for all amino acid residues in the given ''range'' grid searches ~~for fragments defined by~~ the backbone ~~torsion~~ angles φ, ψ and the given side chain ''angles''. To specify more than one side-chain angle, the names must be given, separated by blanks and enclosed in double quotes. If the cutoff value ~~''tfcut''~~ for the local, fragment-based target function is positive, then all conformations with a local target function value below ~~''tfcut''~~ will be considered as allowed. Otherwise, a conformation will be allowed if no single restraint violation exceeds the corresponding cutoff value defined by the variables [[CYANA Variables: soft_upl\|'''soft_upl''']], [[CYANA Variables: soft_lol\|'''soft_lol''']], etc. Unless the '''continue''' option is set, the allowed ranges of ~~torsion~~ angles will be initialized to allow all possible angle values before the grid searches are started. This ~~command~~ provides the ~~functionality~~ of the former ~~HABAS~~ program (Güntert et al., 1989). The results include ~~torsion~~ angle restraints and, if possible, stereospecific assignments for the diastereotopic groups in the fragment. ~~For example,~~		Performs for all amino acid residues in the given ''range'' grid searches comprising the backbone dihedral angles φ, ψ and the given side chain ''angles''. To specify more than one side-chain angle, the names must be given, separated by blanks and enclosed in double quotes. If the cutoff value for the local, fragment-based target function, fmax, is positive, then all conformations with a local target function value below fmax will be considered as allowed. Otherwise, a conformation will be allowed if no single restraint violation exceeds the corresponding cutoff value defined by the variables [[CYANA Variables: soft_upl\|'''soft_upl''']], [[CYANA Variables: soft_lol\|'''soft_lol''']], etc. Unless the '''continue''' option is set, the allowed ranges of dihedral angles will be initialized to allow all possible angle values before the grid searches are started. This macro provides the functions of the former Habas program (Güntert et al., 1989). The results include dihedral angle restraints and, if possible, stereospecific assignments for the diastereotopic groups in the fragment.
	'''habas angles=”CHI1 CHI2*” tfcut=0.05'''
	~~performs~~ grid searches for all amino acid residues including the ~~torsion~~ angles φ, ψ, χ<sup>1</sup> and χ<sup>2</sup>. ~~allowing~~ conformations with local target function values up to 0.05 ~~Å<sup>2</sup>~~.		'''habas angles=”CHI1 CHI2*” tfcut=0.05''' Perform grid searches for all amino acid residues including the dihedral angles φ, ψ, χ<sup>1</sup> and χ<sup>2</sup>. Allow conformations with local target function values up to 0.05.

Masayo: /* Description */

2009-08-13T11:54:07Z

Description

← Older revision		Revision as of 13:54, 13 August 2009
Line 11:		Line 11:
	Performs for all amino acid residues in the given ''range'' grid searches for fragments defined by the backbone torsion angles φ, ψ and the given side chain ''angles''. To specify more than one side-chain angle, the names must be given, separated by blanks and enclosed in double quotes. If the cutoff value ''tfcut'' for the local, fragment-based target function is positive, then all conformations with a local target function value below ''tfcut'' will be considered as allowed. Otherwise, a conformation will be allowed if no single restraint violation exceeds the corresponding cutoff value defined by the variables [[CYANA Variables: soft_upl\|'''soft_upl''']], [[CYANA Variables: soft_lol\|'''soft_lol''']], etc. Unless the '''continue''' option is set, the allowed ranges of torsion angles will be initialized to allow all possible angle values before the grid searches are started. This command provides the functionality of the former HABAS program (Güntert et al., 1989). The results include torsion angle restraints and, if possible, stereospecific assignments for the diastereotopic groups in the fragment. For example,		Performs for all amino acid residues in the given ''range'' grid searches for fragments defined by the backbone torsion angles φ, ψ and the given side chain ''angles''. To specify more than one side-chain angle, the names must be given, separated by blanks and enclosed in double quotes. If the cutoff value ''tfcut'' for the local, fragment-based target function is positive, then all conformations with a local target function value below ''tfcut'' will be considered as allowed. Otherwise, a conformation will be allowed if no single restraint violation exceeds the corresponding cutoff value defined by the variables [[CYANA Variables: soft_upl\|'''soft_upl''']], [[CYANA Variables: soft_lol\|'''soft_lol''']], etc. Unless the '''continue''' option is set, the allowed ranges of torsion angles will be initialized to allow all possible angle values before the grid searches are started. This command provides the functionality of the former HABAS program (Güntert et al., 1989). The results include torsion angle restraints and, if possible, stereospecific assignments for the diastereotopic groups in the fragment. For example,
	'''habas angles=”CHI1 CHI2*” tfcut=0.05'''		'''habas angles=”CHI1 CHI2*” tfcut=0.05'''
	performs grid searches for all amino acid residues including the torsion angles φ, ψ, Χ<sup>1</sup> and Χ<sup>2</sup>. allowing conformations with local target function values up to 0.05 Å<sup>2</sup>.		performs grid searches for all amino acid residues including the torsion angles φ, ψ, χ<sup>1</sup> and χ<sup>2</sup>. allowing conformations with local target function values up to 0.05 Å<sup>2</sup>.

Masayo: /* Description */

2009-08-12T11:29:36Z

Description

← Older revision		Revision as of 13:29, 12 August 2009
Line 9:		Line 9:
	== Description ==		== Description ==

	Performs for all amino acid residues in the given ''range'' grid searches for fragments defined by the backbone torsion angles φ, ψ and the given side chain ''angles''. To specify more than one side-chain angle, the names must be given, separated by blanks and enclosed in double quotes. If the cutoff value ''tfcut'' for the local, fragment-based target function is positive, then all conformations with a local target function value below ''tfcut'' will be considered as allowed. Otherwise, a conformation will be allowed if no single restraint violation exceeds the corresponding cutoff value defined by the variables '''soft_upl''', '''soft_lol''', etc. Unless the '''continue''' option is set, the allowed ranges of torsion angles will be initialized to allow all possible angle values before the grid searches are started. This command provides the functionality of the former HABAS program (Güntert et al., 1989). The results include torsion angle restraints and, if possible, stereospecific assignments for the diastereotopic groups in the fragment. For example,		Performs for all amino acid residues in the given ''range'' grid searches for fragments defined by the backbone torsion angles φ, ψ and the given side chain ''angles''. To specify more than one side-chain angle, the names must be given, separated by blanks and enclosed in double quotes. If the cutoff value ''tfcut'' for the local, fragment-based target function is positive, then all conformations with a local target function value below ''tfcut'' will be considered as allowed. Otherwise, a conformation will be allowed if no single restraint violation exceeds the corresponding cutoff value defined by the variables [[CYANA Variables: soft_upl\|'''soft_upl''']], [[CYANA Variables: soft_lol\|'''soft_lol''']], etc. Unless the '''continue''' option is set, the allowed ranges of torsion angles will be initialized to allow all possible angle values before the grid searches are started. This command provides the functionality of the former HABAS program (Güntert et al., 1989). The results include torsion angle restraints and, if possible, stereospecific assignments for the diastereotopic groups in the fragment. For example,
	'''habas angles=”CHI1 CHI2*” tfcut=0.05'''		'''habas angles=”CHI1 CHI2*” tfcut=0.05'''
	performs grid searches for all amino acid residues including the torsion angles φ, ψ, Χ<sup>1</sup> and Χ<sup>2</sup>. allowing conformations with local target function values up to 0.05 Å<sup>2</sup>.		performs grid searches for all amino acid residues including the torsion angles φ, ψ, Χ<sup>1</sup> and Χ<sup>2</sup>. allowing conformations with local target function values up to 0.05 Å<sup>2</sup>.

Masayo: /* Description */

2009-08-07T09:55:07Z

Description

@@ Line 9: / Line 9: @@
 == Description ==
-Performs for all amino acid residues in the given range grid searches
+Performs for all amino acid residues in the given ''range'' grid searches for fragments defined by the backbone torsion angles φ, ψ and the given side chain ''angles''. To specify more than one side-chain angle, the names must be given, separated by blanks and enclosed in double quotes. If the cutoff value ''tfcut'' for the local, fragment-based target function is positive, then all conformations with a local target function value below ''tfcut'' will be considered as allowed. Otherwise, a conformation will be allowed if no single restraint violation exceeds the corresponding cutoff value defined by the variables '''soft_upl''', '''soft_lol''', etc. Unless the '''continue''' option is set, the allowed ranges of torsion angles will be initialized to allow all possible angle values before the grid searches are started. This command provides the functionality of the former HABAS program (Güntert et al., 1989). The results include torsion angle restraints and, if possible, stereospecific assignments for the diastereotopic groups in the fragment. For example,
-comprising the backbone dihedral angles f, y and the given side-chain
+ '''habas angles=”CHI1 CHI2*” tfcut=0.05'''
-angles. To specify more than one side-chain angle, the names must be
+performs grid searches for all amino acid residues including the torsion angles φ, ψ, Χ<sup>1</sup> and Χ<sup>2</sup>. allowing conformations with local target function values up to 0.05 Å<sup>2</sup>.

Admin: 1 revision

2009-01-29T11:26:59Z

1 revision

New page

== Parameters ==

; range=''integer range'': (default: ''all residues'')
; angles=''string'': (default: CHI1)
; tfcut=''real'': (default: 0.0)
; continue

== Description ==

Performs for all amino acid residues in the given range grid searches
comprising the backbone dihedral angles f, y and the given side-chain
angles. To specify more than one side-chain angle, the names must be
given, separated by blanks and enclosed in double quotes. If the cutoff
value for the local, fragment-based target function, fmax, is positive,
then all conformations with a local target function value below fmax will
be considered as allowed. Otherwise, a conformation will be allowed if no
single restraint violation exceeds the corresponding cutoff value defined
by the variables soft_upl, soft_lol, etc. Unless the continue option is
set, the allowed ranges of dihedral angles will be initialized to allow
all possible angle values before the grid searches are started.
This macro provides the functions of the former Habas program (Guntert et
al., 1989). The results include dihedral angle restraints and, if
possible, stereospecific assignments for the diastereotopic groups in the
fragment.

habas angles="CHI1 CHI2*" tfcut=0.05
Perform grid searches for all amino acid residues including the dihedral
angles f, y, c1 and c2. Allow conformations with local target function
values up to 0.05.