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New Plugin ProBiS H2O is a new plugin for identification of conserved waters in protein structures.
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New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
Older News See Older News.
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Orient

orient aligns the principal components of the atoms in the selection with the XYZ axes. The function is similar to the orient command in X-PLOR.

USAGE

orient object-or-selection [, state]
orient (selection)

PYMOL API

cmd.orient( string object-or-selection [, state = 0] )

NOTES

  state = 0 (default) use all coordinate states
  state = -1 use only coordinates for the current state
  state > 0  use coordinates for a specific state

EXAMPLES

For models with NCS symmetry, orient will align the model with the symmetry axis centered along the viewport's z axis. For example,

  fetch 1hiw, async=0
  as cartoon
  remove (!chain A,B,C)
  orient
  util.cbc

will produce the first image below. However, if there is a larger symmetry, e.g. two trimers, this will not work. In the above example, leaving out remove (!chain A,B,C) from the script results in the second image below. <gallery> Image:1hiw orient.png|One trimer from 1hiw after "orient" ..→

A Random PyMOL-generated Cover. See Covers.