CYANA Command: distances modify - Revision history

Guentert at 11:00, 1 March 2023

2023-03-01T11:00:33Z

New page

== Parameters ==

; pseudoonly

== Description ==

Modifies distance restraints. Distance limits with diastereotopic groups are adjusted and/or pseudoatoms are inserted if no stereospecific assignment is available. Unless the option '''pseudoonly''' is set, redundant and meaningless distance restraints are removed, too.<br>
This command cannot be used for ambiguous distance restraints.<br>
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 (Güntert et al., 1991a; Güntert et al., 1991b). For example:

Modifications for floating stereospecific assignments:
Input restraint(s) modified to
Atom(s) A Atom(s) B1-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 HN 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 - HN 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 - HN 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 9 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 7.3
Upper HN GLU 6 - HG2/3 GLU 6 5.04 5.50 5.50 5.14
Upper HA GLU 6 - HG2/3 GLU 6 4.23

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 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. If the modified distance limit(s) would be meaningless, it is discarded and not reported.
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 include restraints between geminal hydrogen atoms, or between atoms of the same aromatic ring.
:; '''no restriction''' : The restraint is such that no conformation exists that would violate it. The program can detect this only if the restrained distance depends on one or two torsion angles. Many meaningless intraresidual peaks can thus be eliminated.
:; '''duplicate restraint''' : The same restraint occurs more than once in the input, for example because transposed peaks were present in the peak list. Only the most restrictive of these restraints is kept.

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

Further reading:

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

== See also ==

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

Masayo: /* Description */

2009-08-07T13:27:02Z

Description

← Older revision		Revision as of 15:27, 7 August 2009
Line 30:		Line 30:
	Upper HN GLU 6 - HG2/3 GLU 6 5.04 5.50 5.50 5.14		Upper HN GLU 6 - HG2/3 GLU 6 5.04 5.50 5.50 5.14
	Upper HA GLU 6 - HG2/3 GLU 6 4.23		Upper HA GLU 6 - HG2/3 GLU 6 4.23



	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 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.		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 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.
Line 51:		Line 49:
	Number of modified restraints: 597		Number of modified restraints: 597

	Distance restraints can be meaningless for one of the following		Distance restraints can be meaningless for one of the following reasons:
	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		:; '''fixed distance''' : The restraint concerns an interatomic distance that cannot be varied by changing the rotatable torsion angles. Examples include restraints between geminal hydrogen atoms, or between atoms of the same aromatic ring.
	conformation that would violate it. The program		:; '''no restriction''' : The restraint is such that no conformation exists that would violate it. The program can detect this only if the restrained distance depends on one or two torsion angles. Many meaningless intraresidual peaks can thus be eliminated.
	can detect this only if the restrained distance		:; '''duplicate restraint''' : The same restraint occurs more than once in the input, for example because transposed peaks were present in the peak list. Only the most restrictive of these restraints is kept.
	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		The number of upper distance limits after the modifications is given at the end of the table. Depending on the extent of stereospecific assignments etc., the '''distances modify''' command may increase or decrease the number of restraints.
	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:		Further reading:

Masayo: /* Description */

2009-08-07T13:24:15Z

Description

@@ Line 6: / Line 6: @@
 == Description ==
-This command modifies distance restraints. Distance limits with
+Modifies distance restraints. Distance limits with diastereotopic groups are adjusted and/or pseudoatoms are inserted if no stereospecific assignment is available. Unless the option '''pseudoonly''' is set, redundant and meaningless distance restraints are removed, too.<br>
-diastereotopic groups are adjusted and/or pseudo atoms are inserted
+This command cannot be used for ambiguous distance restraints.<br>
-if no stereospecific assignment is available. Unless the option
+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 (Güntert et al., 1991a; Güntert et al., 1991b). For example:
-This command cannot be used for ambiguous distance restraints.
+ Modifications for floating stereospecific assignments:
-        Atom(s) A      Atom(s) B      Input restraint(s)      modified to
+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 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.
-                                      A1-B1 A1-B2 A2-B1 A2-B2 Ai-Bj QA-QB
+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. If the modified distance limit(s) would be meaningless, it is discarded and not reported.
-  Upper HA     ASP 1 - HD2/3  PRO  2        3.39              3.55
+A second table reports redundant and meaningless restraints that are removed. For example:
    Meaningless distance restraints:

Admin: 1 revision

2009-01-29T11:26:55Z

1 revision

New page

== Parameters ==

; pseudoonly

== Description ==

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]]