Distances modify - Revision history

Admin: 1 revision

2009-01-28T18:18:39Z

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	= ~~distances modify~~ =		= distances_modify =

	== Parameters ==		== Parameters ==

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2009-01-28T18:12:27Z

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			= distances modify =

	== Parameters ==		== Parameters ==

Admin: 1 revision

2009-01-28T17:25:56Z

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	~~Modify distance restraints~~

	Parameters: pseudoonly		== Parameters ==

			; pseudoonly

			== Description ==

	This command modifies distance restraints. Distance limits with		This command modifies distance restraints. Distance limits with
	diastereotopic groups are adjusted and/or pseudo atoms are inserted		diastereotopic groups are adjusted and/or pseudo atoms are inserted
	if no stereospecific assignment is available. Unless the option		if no stereospecific assignment is available. Unless the option
	'pseudoonly' is set, redundant and meaningless distance restraints		'''pseudoonly''' is set, redundant and meaningless distance restraints
	are removed, too.		are removed, too.

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	A detailed report of the modifications made is provided if the		A detailed report of the modifications made is provided if the
	information level is full ('info=full'). A first table reports the		information level is full ('''info=full'''). A first table reports the
	modifications made to make distance restraints symmetric under the		modifications made to make distance restraints symmetric under the
	exchange of diastereotopic partners in order to account for the		exchange of diastereotopic partners in order to account for the
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	* Guntert et al. J. Mol. Biol. 217, 531-540 (1991).		* Guntert et al. J. Mol. Biol. 217, 531-540 (1991).

	== See also ==		== See also ==

	* [[distance multiple]]		* [[distance multiple]]
	* [[distance unique]]		* [[distance unique]]

Admin: /* See also */

2009-01-28T12:35:03Z

Admin: /* See also */

2009-01-28T12:34:52Z

Admin at 12:34, 28 January 2009

2009-01-28T12:34:37Z

← Older revision		Revision as of 14:34, 28 January 2009
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	~~6CYANA: distances modify - CYANA command~~		Modify distance restraints

	Parameters: pseudoonly		Parameters: pseudoonly
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	Further reading:		Further reading:

	- Guntert et al. J. Mol. Biol. 217, 517-530 (1991).		* Guntert et al. J. Mol. Biol. 217, 517-530 (1991).
	- Guntert et al. J. Mol. Biol. 217, 531-540 (1991).		* Guntert et al. J. Mol. Biol. 217, 531-540 (1991).

	See also: distance multiple, distance unique		== See also ==

			[[distance multiple]]
			[[distance unique]]

Admin: New page: 6CYANA: distances modify - CYANA command Parameters: pseudoonly This command modifies distance restraints. Distance limits with diastereotopic groups are adjusted an...

2009-01-28T12:32:39Z

New page: 6CYANA: distances modify - CYANA command Parameters: pseudoonly This command modifies distance restraints. Distance limits with diastereotopic groups are adjusted an...

New page

6CYANA: distances modify - CYANA command

Parameters: pseudoonly

This command modifies distance restraints. Distance limits with
diastereotopic groups are adjusted and/or pseudo atoms are inserted
if no stereospecific assignment is available. Unless the option
'pseudoonly' is set, redundant and meaningless distance restraints
are removed, too.

This command cannot be used for ambiguous distance restraints.

A detailed report of the modifications made is provided if the
information level is full ('info=full'). A first table reports the
modifications made to make distance restraints symmetric under the
exchange of diastereotopic partners in order to account for the
absence of stereospecific assignments. For example:

Modifications for floating stereospecific assignments:

Atom(s) A Atom(s) B Input restraint(s) modified to
A1-B1 A1-B2 A2-B1 A2-B2 Ai-Bj QA-QB
Upper HA ASP 1 - HD2/3 PRO 2 3.39 3.55
Upper HB2/3 ASP 1 - HD2/3 PRO 2 5.50 5.50 3.89 5.41 5.50 4.97
Upper HB2 PRO 2 - HG2/3 MET 3 5.50 6.38
Upper HD2/3 PRO 2 - QE TYR 19 7.63 8.51
Upper H MET 3 - HB2/3 MET 3 3.95 3.33 3.83 3.45
Upper HB2/3 MET 3 - QE MET 3 6.53 6.31 6.53
Upper HB2/3 MET 3 - H THR 4 5.38 5.50 5.50
Upper HB2/3 MET 3 - HA THR 4 4.69 5.54
Upper HG2/3 MET 3 - H THR 4 4.14 5.01
Upper HG2/3 MET 3 - HB THR 4 5.50 6.38
Upper HG2/3 MET 3 - QB ALA 8 6.53 7.40
Upper HG2/3 MET 3 - QD TYR 19 7.64 8.52
Upper HG2/3 MET 3 - QE TYR 19 7.63 8.51
Upper QE MET 3 - HG2/3 MET 16 5.47 6.35
Upper QG2 THR 4 - HE21/2 GLN 7 6.53 7.39
Upper H GLU 6 - HG2/3 GLU 6 5.04 5.50 5.50 5.14

Each line in the listing of distance restraint modifications treats a
pair of distance restraints in case one diastereotopic pair (without
stereospecific assignment) is involved, or a group of up to four of
distance restraints in case two diastereotopic pairs are involved. The
input restraints are listed in the columns A1-B1, A1-B2, A2-B1 and
A2-B2, where A1 denotes the first atom of the first diastereotopic
group, A2 the second atom of the first diastereotopic group, B1 the
first atom of the second diastereotopic group, and B2 the second atom
of the second diastereotopic group.

These will then be replaced by the distance restraints listed in the
two columns Ai-Bj and QA-QB. A number in the Ai-Bj column indicates
that equal distance restraints with this upper bound are applied to
all two or four individual distances that involve the diastereotopic
substituents. A number given in the QA-QB column indicates the single
upper distance bound that is applied to the distance to the pseudoatom,
or between the two pseudoatoms in the case of two prochiral groups.

A second table reports redundant and meaningless restraints that
are removed. For example:

Meaningless distance restraints:
limit diagnosis
Upper HA ASP 1 - HB3 ASP 1 3.21 duplicate restraint
Upper HA ASP 1 - HB3 ASP 1 3.21 no restriction
Upper HA ASP 1 - HD2 PRO 2 4.20 duplicate restraint
Upper HA ASP 1 - HD2 PRO 2 4.20 no restriction
Upper HA ASP 1 - HD3 PRO 2 3.21 duplicate restraint
Upper HB2 ASP 1 - HB3 ASP 1 2.40 duplicate restraint
Upper HB2 ASP 1 - HB3 ASP 1 2.40 fixed distance
Upper HB2 ASP 1 - HD2 PRO 2 5.50 duplicate restraint
...
Number of modified restraints: 597

Distance restraints can be meaningless for one of the following
reasons:

fixed distance The restraint concerns an interatomic distance that
cannot be varied by changing the rotatable torsion
angles. Examples of this sort are restraints between
geminal hydrogen atoms, or restraints between atoms
of the same aromatic ring.

no restriction The restraint is such that there exists no
conformation that would violate it. The program
can detect this only if the restrained distance
depends on one or two dihedral angles.

duplicate restraint The same restraint occurs more than once in the
input, for instance because transposed peaks were
present in the peak list. The most restrictive
restraint is kept in this case.

The number of upper distance limits after the modifications is given
at the end of the table. Depending on the number of stereospecific
assignments, the modifications may increase or decrease the number
of restraints.

Further reading:

- Guntert et al. J. Mol. Biol. 217, 517-530 (1991).
- Guntert et al. J. Mol. Biol. 217, 531-540 (1991).

See also: distance multiple, distance unique

← Older revision		Revision as of 14:35, 28 January 2009
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	== See also ==		== See also ==

	[[distance multiple]]		* [[distance multiple]]
			* [[distance unique]]
	[[distance unique]]