Atoms glomsa

atoms_glomsa

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