CYANA Macro: habas: Difference between revisions
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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, | 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>. | ||
Revision as of 13:54, 13 August 2009
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 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,
habas angles=”CHI1 CHI2*” tfcut=0.05
performs grid searches for all amino acid residues including the torsion angles φ, ψ, χ1 and χ2. allowing conformations with local target function values up to 0.05 Å2.