Miguel, have I got this wrong?
show center
Delivers the coordinates of the center of the model. Units are in Angstroms. Output is in
the form
center: (centerX, centerY, centerZ)
This is static, right? Ooh -- no, it's not. It changes when the molecule is
recentered.
That's interesting -- a way to get the coordinates of a particular atom shown:
center [CYS]4.O;show center;center
It should probably read "current display center"?
Bob
Miguel wrote:
Is there a way to get Jmol to tell me the current centerAt boundbox
coordinates, once I have changed the center by a command such as
"center 124:a.ca" ?
Not sure exactly what you are asking with the phrase 'current centerAt
boundbox'
Here is some stuff in random order that might help:
For a given molecule, the boundbox is always the same. The axes are drawn
from the center of the boundbox to the centers of the faces of the
boundbox. Since the boundbox is always the same the axes are always the
same.
set boundbox on;
set axes on;
With recent versions of Jmol, the default center is the center of the
boundbox. You can show the center coordinates with:
show center;
You can then change the center in a number of ways
center <some-set-of-atoms>; show center;
Or, you can use the centerAt command:
centerAt average; show center;
centerAt boundBox; show center;
centerAt absolute 0 0 0; show center;
It is somewhat complicated, but 'average' and 'boundbox' can also take
relative offsets. In the sample below, the second command will have the
center be 10 anstroms along the X axes to the right of the default
boundbox.
centerAt boundBox; show center;
centerAt boundBox 10 0 0; show center;
Miguel
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