CYANA Command: atoms glomsa - Revision history

Guentert at 07:45, 28 June 2010

2010-06-28T07:45:52Z

← Older revision		Revision as of 09:45, 28 June 2010
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	== Parameters ==		== Parameters ==

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	; cutoff=''real'': (default: 0.4)		; cutoff=''real'': (default: 0.4)
	; threshold=''real'': (default: 0.4)		; threshold=''real'': (default: 0.4)
	; fr		; fraction=''real'': (default: 100.0)
	; single		; single

Masayo: /* Parameters */

2009-08-13T09:49:22Z

Parameters

← Older revision		Revision as of 11:49, 13 August 2009
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	== Parameters ==		== Parameters ==

	; selection=''~~string~~'': (default: ''none'')		; selection=''[[atom selection]]'': (default: ''none'')
	; cutoff=''real'': (default: 0.4)		; cutoff=''real'': (default: 0.4)
	; threshold=''real'': (default: 0.4)		; threshold=''real'': (default: 0.4)
	; fr		; fr
	; single		; single

	== Description ==		== Description ==

Admin: /* Description */

2009-08-06T12:24:13Z

Description

← Older revision		Revision as of 14:24, 6 August 2009
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	== Description ==		== Description ==

	Search for stereospecific assignments of the selected diastereotopic atoms by analyzing the distances that are restrained by upper distance limits in the selected conformers. The command provides the functionality of the former standalone program GLOMSA (“<u>Glo</u>bal <u>m</u>ethod for <u>s</u>tereospecific <u>a</u>ssignments”) (Güntert et al., 1991a; Güntert et al., 1991b). By default, the selection made in the most recent [[CYANA Commands: atoms select\|'''atoms select''']] command is used, or all diastereotopic atoms if no selection has been made so far. Stereospecific assignment proposals are reported for those diastereotopic pairs for which the difference between the upper bounds from the two diastereotopic atoms to a third atom exceeds the ''cutoff'', given in Å, and the corresponding average distance difference in the selected conformers is larger than the threshold, also given in Å, in at least the chosen ''fraction'', given in percent, of the selected conformers. Single distance restraints from one but not the other of two diastereotopic partners to a third atom can be considered by setting the option '''single'''. The ~~[[CYANA Commands: atoms glomsa\|~~'''atoms glomsa''']] command reports proposals for stereospecific assignments but does not fix the stereospecific assignment as the [[CYANA Commands: atoms stereo\|'''atoms stereo''']] command.		Search for stereospecific assignments of the selected diastereotopic atoms by analyzing the distances that are restrained by upper distance limits in the selected conformers. The command provides the functionality of the former standalone program GLOMSA (“<u>Glo</u>bal <u>m</u>ethod for <u>s</u>tereospecific <u>a</u>ssignments”) (Güntert et al., 1991a; Güntert et al., 1991b). By default, the selection made in the most recent [[CYANA Commands: atoms select\|'''atoms select''']] command is used, or all diastereotopic atoms if no selection has been made so far. Stereospecific assignment proposals are reported for those diastereotopic pairs for which the difference between the upper bounds from the two diastereotopic atoms to a third atom exceeds the ''cutoff'', given in Å, and the corresponding average distance difference in the selected conformers is larger than the threshold, also given in Å, in at least the chosen ''fraction'', given in percent, of the selected conformers. Single distance restraints from one but not the other of two diastereotopic partners to a third atom can be considered by setting the option '''single'''. The '''atoms glomsa''' command reports proposals for stereospecific assignments but does not fix the stereospecific assignment as the [[CYANA Commands: atoms stereo\|'''atoms stereo''']] command.

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

Admin: /* See also */

2009-08-06T12:23:33Z

Admin: /* Description */

2009-08-06T12:19:29Z

Description

← Older revision		Revision as of 14:19, 6 August 2009
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	== Description ==		== Description ==

	Search for stereospecific assignments of the selected diastereotopic atoms by analyzing the distances that are restrained by upper distance limits in the selected conformers. The command provides the functionality of the former standalone program GLOMSA (~~“Global method~~ for ~~stereospecific assignments”~~) (Güntert et al., 1991a; Güntert et al., 1991b). By default, the selection made in the most recent [[CYANA Commands: atoms select\|'''atoms select''']] command is used, or all diastereotopic atoms if no selection has been made so far. Stereospecific assignment proposals are reported for those diastereotopic pairs for which the difference between the upper bounds from the two diastereotopic atoms to a third atom exceeds the ''cutoff'', given in Å, and the corresponding average distance difference in the selected conformers is larger than the threshold, also given in Å, in at least the chosen ''fraction'', given in percent, of the selected conformers. Single distance restraints from one but not the other of two diastereotopic partners to a third atom can be considered by setting the option '''single'''. The [[CYANA Commands: atoms glomsa\|'''atoms glomsa''']] command reports proposals for stereospecific assignments but does not fix the stereospecific assignment as the [[CYANA Commands: atoms stereo\|'''atoms stereo''']] command.		Search for stereospecific assignments of the selected diastereotopic atoms by analyzing the distances that are restrained by upper distance limits in the selected conformers. The command provides the functionality of the former standalone program GLOMSA (“<u>Glo</u>bal <u>m</u>ethod for <u>s</u>tereospecific <u>a</u>ssignments”) (Güntert et al., 1991a; Güntert et al., 1991b). By default, the selection made in the most recent [[CYANA Commands: atoms select\|'''atoms select''']] command is used, or all diastereotopic atoms if no selection has been made so far. Stereospecific assignment proposals are reported for those diastereotopic pairs for which the difference between the upper bounds from the two diastereotopic atoms to a third atom exceeds the ''cutoff'', given in Å, and the corresponding average distance difference in the selected conformers is larger than the threshold, also given in Å, in at least the chosen ''fraction'', given in percent, of the selected conformers. Single distance restraints from one but not the other of two diastereotopic partners to a third atom can be considered by setting the option '''single'''. The [[CYANA Commands: atoms glomsa\|'''atoms glomsa''']] command reports proposals for stereospecific assignments but does not fix the stereospecific assignment as the [[CYANA Commands: atoms stereo\|'''atoms stereo''']] command.

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

Admin: /* Description */

2009-08-06T12:09:37Z

Description

← Older revision		Revision as of 14:09, 6 August 2009
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	== Description ==		== Description ==

	Search for stereospecific assignments of the selected diastereotopic atoms by analyzing the distances that are restrained by upper distance limits in the selected conformers. The command provides the functionality of the former standalone program GLOMSA (~~“[[Glo]]bal [[m]]ethod~~ for ~~[[s]]tereospecific [[a]]ssignments”~~) (Güntert et al., 1991a; Güntert et al., 1991b). By default, the selection made in the most recent [[CYANA Commands: atoms select\|'''atoms select''']] command is used, or all diastereotopic atoms if no selection has been made so far. Stereospecific assignment proposals are reported for those diastereotopic pairs for which the difference between the upper bounds from the two diastereotopic atoms to a third atom exceeds the ''cutoff'', given in Å, and the corresponding average distance difference in the selected conformers is larger than the threshold, also given in Å, in at least the chosen ''fraction'', given in percent, of the selected conformers. Single distance restraints from one but not the other of two diastereotopic partners to a third atom can be considered by setting the option '''single'''. The [[CYANA Commands: atoms glomsa\|'''atoms glomsa''']] command reports proposals for stereospecific assignments but does not fix the stereospecific assignment as the [[CYANA Commands: atoms stereo\|'''atoms stereo''']] command.		Search for stereospecific assignments of the selected diastereotopic atoms by analyzing the distances that are restrained by upper distance limits in the selected conformers. The command provides the functionality of the former standalone program GLOMSA (“Global method for stereospecific assignments”) (Güntert et al., 1991a; Güntert et al., 1991b). By default, the selection made in the most recent [[CYANA Commands: atoms select\|'''atoms select''']] command is used, or all diastereotopic atoms if no selection has been made so far. Stereospecific assignment proposals are reported for those diastereotopic pairs for which the difference between the upper bounds from the two diastereotopic atoms to a third atom exceeds the ''cutoff'', given in Å, and the corresponding average distance difference in the selected conformers is larger than the threshold, also given in Å, in at least the chosen ''fraction'', given in percent, of the selected conformers. Single distance restraints from one but not the other of two diastereotopic partners to a third atom can be considered by setting the option '''single'''. The [[CYANA Commands: atoms glomsa\|'''atoms glomsa''']] command reports proposals for stereospecific assignments but does not fix the stereospecific assignment as the [[CYANA Commands: atoms stereo\|'''atoms stereo''']] command.

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

Admin: /* Description */

2009-08-06T12:08:20Z

Description

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 == Description ==
-The '''atoms glomsa''' command searches for stereospecific assignments of
+Search for stereospecific assignments of the selected diastereotopic atoms by analyzing the distances that are restrained by upper distance limits in the selected conformers. The command provides the functionality of the former standalone program GLOMSA (“[[Glo]]bal [[m]]ethod for [[s]]tereospecific [[a]]ssignments”) (Güntert et al., 1991a; Güntert et al., 1991b). By default, the selection made in the most recent [[CYANA Commands: atoms select|'''atoms select''']] command is used, or all diastereotopic atoms if no selection has been made so far.  Stereospecific assignment proposals are reported for those diastereotopic pairs for which the difference between the upper bounds from the two diastereotopic atoms to a third atom exceeds the ''cutoff'', given in Å, and the corresponding average distance difference in the selected conformers is larger than the threshold, also given in Å, in at least the chosen ''fraction'', given in percent, of the selected conformers. Single distance restraints from one but not the other of two diastereotopic partners to a third atom can be considered by setting the option '''single'''. The [[CYANA Commands: atoms glomsa|'''atoms glomsa''']] command reports proposals for stereospecific assignments but does not fix the stereospecific assignment as the [[CYANA Commands: atoms stereo|'''atoms stereo''']] command.
 == See also ==

Admin: 1 revision

2009-01-29T11:26:54Z

1 revision

New page

== Parameters ==

; selection=''string'': (default: ''none'')
; cutoff=''real'': (default: 0.4)
; threshold=''real'': (default: 0.4)
; fr
; single

== Description ==

The '''atoms glomsa''' command searches for stereospecific assignments of
diastereotopic atoms matched by the selection ''string'' by analyzing
the distances that are restrained by an upper distance limit in the
selected conformers. The command provides the functionality of the
former separate program GLOMSA ("GLObal Method for Stereospecific
Assignments"). By default, the selection made in the most recent '''atoms
select''' command is used, or all diastereotopic atoms if no selection
has been made so far. Stereospecific assignment proposals are reported
for those diastereotopic pairs for which the difference between the
upper bounds from the two diastereotopic atoms to a third atom exceeds
the ''cutoff'', given in Angstrom, and the corresponding average distance
difference in the selected conformers is larger than the ''threshold'',
also given in Angstrom, in at least the chosen ''fraction'', given in
percent, of the selected conformers. Single distance restraints from
one but not the other of two diastereotopic partners to a third atom
can be considered by setting the option '''single'''. The '''atoms glomsa'''
command reports proposals for stereospecific assignments but does
not fix the stereospecific assignment as the '''atoms stereo''' command.

Further reading:

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

== See also ==

* [[atoms stereo]]
* [[stereoassign]]
* [[habas]]

← Older revision		Revision as of 14:23, 6 August 2009
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	== See also ==		== See also ==

	* [[atoms stereo]]		* [[CYANA Commands: atoms stereo\|'''atoms stereo''']]
	* [[stereoassign]]		* [[CYANA Macro: stereoassign\|'''stereoassign''']]
	* [[habas]]		* [[CYANA Macro: habas\|'''habas''']]