Difference between revisions of "Orient"
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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. | '''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]] |
− | [[Category:Commands| | + | [[Category:Commands|Orient]] |
+ | [[Category:States|Orient]] | ||
+ | [[Category:View Module|Orient]] |
Latest revision as of 13:35, 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.