Orient: Difference between revisions
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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=== | ===USAGE=== | ||
orient object-or-selection [, state] | |||
orient (selection) | |||
===PYMOL API=== | ===PYMOL API=== | ||
<source lang="python"> | |||
cmd.orient( string object-or-selection [, state = 0] ) | |||
</source> | |||
===NOTES=== | ===NOTES=== | ||
state = 0 (default) use all coordinate states | state = 0 (default) use all coordinate states | ||
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]] | |||
[[Category:Commands|Orient]] | |||
[[Category:Commands| | [[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.
One trimer from 1hiw after "orient" command.
Both trimers from 1hiw after "orient" command.
