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2014-03-28T02:16:34Z

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Jaredsampson: /* EXAMPLES */ added a second image and `tags`


2010-09-07T17:35:19Z
EXAMPLES:  added a second image and <code> tags
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'''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===

<source lang="python">

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

</source>



===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 <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===

[[Zoom]], [[Origin]], [[Reset]]



[[Category:Commands|Orient]]

[[Category:States|Orient]]

[[Category:View Module|Orient]]

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Jaredsampson: /* EXAMPLES */ added a second image and tags

Jaredsampson: /* EXAMPLES */ added a second image and `tags`