Orient: Difference between revisions
Jump to navigation
Jump to search
mNo edit summary |
Jaredsampson (talk | contribs) (→EXAMPLES: added a second image and <code> tags) |
||
| (2 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
'''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. | ||
| Line 15: | Line 14: | ||
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=== | ||
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.
