CYANA Command: grid search: Difference between revisions
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== Description == | == Description == | ||
Performs a grid search for the current fragment (as defined by the most recent [[CYANA Commands: grid fragment|'''grid fragment''']] command). The grid search will be done over all torsion angles in the fragment and with the number of steps per torsion angle given by the variable '''nstep'''. 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 “soft” cutoff values defined by the variables [[CYANA Variables: soft_upl|'''soft_upl''']], [[CYANA Variables: soft_lol|'''soft_lol''']], [[CYANA Variables: soft_vdw|'''soft_vdw''']], [[CYANA Variables: soft_aco|'''soft_aco''']], and [[CYANA Variables: soft_cco|'''soft_cco''']]. Other types of restraints, e.g. residual dipolar couplings or pseudocontact shifts, cannot be used in grid searches. The grid search is restricted to angle values that are allowed according to the standard grid memory, '''A'''. The resulting allowed angle values from the grid search will again be stored in the standard grid memory, '''A'''. | |||
defined by the most recent '''grid fragment''' command). The grid search | To avoid excessive computation times for fragments with many angles and/or few restraints, the calculation is not started if the expected number of grid points to be checked (after the evaluation of restraints that involve a single torsion angle) exceeds the value of the variable [[CYANA Variables: gridpoints|'''gridpoints''']]. Similarly, a grid search is aborted if the estimated total computation time in seconds exceeds '''gridtime''' seconds. | ||
will be done over all torsion angles in the fragment and with the | If the '''test''' option is set, the grid search will not be started but the expected number of grid points to be checked (after evaluation of the restraints that depend on a single dihedral angle) will be reported. | ||
number of steps per torsion angle given by the variable '''nstep'''. If | |||
the cutoff value | |||
target function is positive, then all conformations with a local | |||
target function value below | |||
allowed. Otherwise, a conformation will be allowed if no single | |||
restraint violation exceeds the corresponding | |||
defined by the variables soft_upl, soft_lol, soft_vdw, soft_aco, and | |||
soft_cco. Other types of restraints, e.g. residual dipolar couplings | |||
or pseudocontact shifts, cannot be used in grid searches. | |||
To avoid excessive computation times for fragments with many angles | |||
and/or few restraints, the calculation is not started if the expected | |||
number of grid points to be checked (after the evaluation of restraints | |||
that involve a single torsion angle) exceeds the value of the variable | |||
'''gridpoints'''. Similarly, a grid search is aborted if the estimated | |||
total computation time in seconds exceeds gridtime seconds | |||
If the '''test''' option is set, the grid search will not be started but | |||
the expected number of grid points to be checked (after evaluation | |||
of the restraints that depend on a single dihedral angle) will be | |||
reported. | |||
The grid search is restricted to angle values that are allowed | The grid search is restricted to angle values that are allowed | ||
Latest revision as of 12:42, 12 August 2009
Parameters
- tfcut=real
- (default: 0.0)
- test
Description
Performs a grid search for the current fragment (as defined by the most recent grid fragment command). The grid search will be done over all torsion angles in the fragment and with the number of steps per torsion angle given by the variable nstep. 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 “soft” cutoff values defined by the variables soft_upl, soft_lol, soft_vdw, soft_aco, and soft_cco. Other types of restraints, e.g. residual dipolar couplings or pseudocontact shifts, cannot be used in grid searches. The grid search is restricted to angle values that are allowed according to the standard grid memory, A. The resulting allowed angle values from the grid search will again be stored in the standard grid memory, A. To avoid excessive computation times for fragments with many angles and/or few restraints, the calculation is not started if the expected number of grid points to be checked (after the evaluation of restraints that involve a single torsion angle) exceeds the value of the variable gridpoints. Similarly, a grid search is aborted if the estimated total computation time in seconds exceeds gridtime seconds. If the test option is set, the grid search will not be started but the expected number of grid points to be checked (after evaluation of the restraints that depend on a single dihedral angle) will be reported.
The grid search is restricted to angle values that are allowed according to the standard grid memory, A. The resulting allowed angle values from the grid search will again be stored in the standard grid memory.
Further reading:
Guntert et al. J. Biomol. NMR 12, 543-548 (1998). Guntert et al. J. Am. Chem. Soc. 111, 3997-4004 (1989).