Orient: Difference between revisions

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===DESCRIPTION===
'''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.
'''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.


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   state = -1 use only coordinates for the current state
   state = -1 use only coordinates for the current state
   state > 0  use coordinates for a specific 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 <code>remove (!chain A,B,C)</code> from the script results in the second image below.
<gallery>
Image:1hiw orient.png|One trimer from 1hiw after "orient" command.
Image:1hiw orient2.png|Both trimers from 1hiw after "orient" command.
</gallery>


===SEE ALSO===
===SEE ALSO===
[[Zoom]], [[Origin]], [[Reset]]
[[Zoom]], [[Origin]], [[Reset]]


[[Category:Commands|orient]]
[[Category:Commands|Orient]]
[[Category:States|Orient]]
[[Category:View Module|Orient]]

Latest revision as of 12:35, 7 September 2010

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.

SEE ALSO

Zoom, Origin, Reset