CYANA Command: atoms glomsa: Difference between revisions
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== Parameters == | == Parameters == | ||
; selection='' | ; 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) | ||
; | ; fraction=''real'': (default: 100.0) | ||
; single | ; single | ||
== 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 '''atoms glomsa''' command reports proposals for stereospecific assignments but does not fix the stereospecific assignment as the [[CYANA Commands: atoms stereo|'''atoms stereo''']] command. | |||
diastereotopic atoms | |||
the distances that are restrained by | |||
selected conformers. The command provides the functionality of the | |||
former | |||
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 | |||
difference in the selected conformers is larger than the | |||
also 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 | |||
== See also == | == See also == | ||
* [[atoms stereo]] | * [[CYANA Commands: atoms stereo|'''atoms stereo''']] | ||
* [[stereoassign]] | * [[CYANA Macro: stereoassign|'''stereoassign''']] | ||
* [[habas]] | * [[CYANA Macro: habas|'''habas''']] | ||
Latest revision as of 08:45, 28 June 2010
Parameters
- selection=atom selection
- (default: none)
- cutoff=real
- (default: 0.4)
- threshold=real
- (default: 0.4)
- fraction=real
- (default: 100.0)
- single
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 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 atoms stereo command.