CYANA Macro: dinucleotide: Difference between revisions
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== Description == | == Description == | ||
Performs grid searches for all dinucleotide fragments in the given range. | Performs grid searches for all dinucleotide fragments in the given ''residue range''. 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. The results include torsion angle restraints and, if possible, stereospecific assignments for the diastereotopic groups in the fragment. | ||
If the cutoff value for the local, fragment-based target function | |||
is positive, then all conformations with a local target function value | |||
below | |||
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 | |||
angles will be initialized to allow all possible angle values before the | |||
grid searches are started. | |||
The results include | |||
stereospecific assignments for the diastereotopic groups in the fragment. | |||
Revision as of 15:56, 7 August 2009
Parameters
- range=integer range
- (default: all residues)
- tfcut=real
- (default: 0.0)
- continue
Description
Performs grid searches for all dinucleotide fragments in the given residue range. 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. The results include torsion angle restraints and, if possible, stereospecific assignments for the diastereotopic groups in the fragment.