CYANA Macro: habas: Difference between revisions
m (1 revision) |
|||
| (4 intermediate revisions by 2 users not shown) | |||
| Line 9: | Line 9: | ||
== Description == | == 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 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. | ||
comprising the backbone dihedral angles | |||
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 ( | |||
al., 1989). The results include dihedral angle restraints and, if | |||
possible, stereospecific assignments for the diastereotopic groups in the | |||
fragment. | |||
habas angles= | '''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. | ||
Perform grid searches for all amino acid residues including the dihedral | |||
angles | |||
values up to 0.05. | |||
Latest revision as of 16:35, 12 January 2010
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 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 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 (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, χ1 and χ2. Allow conformations with local target function values up to 0.05.