CYANA Macro: dinucleotide - Revision history

Miki at 14:51, 12 January 2010

2010-01-12T14:51:17Z

← Older revision		Revision as of 16:51, 12 January 2010
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	== Parameters ==		== Parameters ==

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	== Description ==		== 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 [[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. The results include ~~torsion~~ angle restraints and, if possible, stereospecific assignments for the diastereotopic groups in the fragment.		Performs grid searches for all dinucleotide fragments in the given ''range''. 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, i.e. if fmax = 0.0, 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. The results include dihedral angle restraints and, if possible, stereospecific assignments for the diastereotopic groups in the fragment.

Masayo: /* Description */

2009-08-12T12:10:48Z

Description

← Older revision		Revision as of 14:10, 12 August 2009
Line 8:		Line 8:
	== Description ==		== 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.		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 [[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. The results include torsion angle restraints and, if possible, stereospecific assignments for the diastereotopic groups in the fragment.

Masayo: /* Description */

2009-08-07T13:56:29Z

Description

← Older revision		Revision as of 15:56, 7 August 2009
Line 8:		Line 8:
	== 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~~, fmax,~~
	is positive, then all conformations with a local target function value
	below ~~fmax~~ will be considered as allowed. Otherwise~~, i.e. if fmax = 0.0~~, 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.
	The results include ~~dihedral~~ angle restraints and, if possible,
	stereospecific assignments for the diastereotopic groups in the fragment.

Admin: 1 revision

2009-01-29T11:26:58Z

1 revision

New page

== Parameters ==

; range=''integer range'': (default: ''all residues'')
; tfcut=''real'': (default: 0.0)
; continue

== Description ==

Performs grid searches for all dinucleotide fragments in the given range.
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, i.e. if fmax = 0.0, 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.
The results include dihedral angle restraints and, if possible,
stereospecific assignments for the diastereotopic groups in the fragment.