CYANA Command: grid search - Revision history

Masayo: /* Description */

2009-08-12T11:42:41Z

Description

← Older revision		Revision as of 13:42, 12 August 2009
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	== Description ==		== 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'''.		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'''.
	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.		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.
	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.		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.

Masayo: /* Description */

2009-08-07T11:56:54Z

Description

@@ Line 7: / Line 7: @@
 == Description ==
-This command performs a grid search for the current fragment (as
+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'''.
-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 '''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.
 The grid search is restricted to angle values that are allowed

Admin: 1 revision

2009-01-29T11:26:55Z

1 revision

New page

== Parameters ==

; tfcut=''real'': (default: 0.0)
; test

== Description ==

This command 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 given by the '''tfcut''' for the local, fragment-based
target function is positive, then all conformations with a local
target function value below this cutoff 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.

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
number of grid points to be checked (after evaluation of the restraints
that depend on a single dihedral angle) is larger than Nmax, or if
the estimated computation time for the complete grid search exceeds
tmax seconds, the calculation will be stopped.

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).