# [Chimera-users] Rotation Angle

Eric Pettersen pett at cgl.ucsf.edu
Wed Sep 7 18:55:46 PDT 2005

```Hi Zhong,
When the first model is opened in Chimera and before it has been
moved by the mouse or other means, its coordinate system is the same
as Chimera's coordinate system (if you write out a PDB file at this
point, the atom coordinates will be unchanged).  Once the model is
moved, its coordinates are transformed by the appropriate translation
and rotation matrices to yield transformed coordinates.  Saving a PDB
file would then yield different coordinates than when the structure
is first opened.  Rotation parameters (e.g. xyz center of rotation)
are in the same reference frame as these transformed coordinates.
So, if the transformed coordinates of an atom were (3,4,5) and the
center of rotation was (3,4,5) then the model would be rotating about
that atom.
I should mention that if you open a second model when another
model is open, then the second model will be immediately transformed
by the same rotations and translations that the first model is being
transformed by.  So if you have two structures that are supposed to
be in certain relative positions according to their original
coordinates, they will still be in those same relative positions when
opened in Chimera, even if the first model is moved before the second
model is opened.  With many models open, a new model is transformed
the same as the lowest-numbered model currently open.
The meanings of the various rotation methods are described here:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/
sideview.html#rotation .  There are also various commands/tools to
help in moving models in specific ways.  The Constrained Move tool
(in the Movement category) allows you to use the mouse to translate/
rotate models on specified axes in the _model_ coordinate reference
frame.  The "reset" command moves models back to their positions when
they were originally opened.  The "turn" and "move" commands rotate
and translate active models along/about specific axes in the Chimera
reference frame.
Hope this helps.

Eric Pettersen
UCSF Computer Graphics Lab
pett at cgl.ucsf.edu
http://www.cgl.ucsf.edu

On Sep 7, 2005, at 4:01 PM, Huang, Zhong wrote:

> Hi, dear chimera developers'
>  I am a Chimera user of UT Medical school at Houston . Here I want
> to know how chimera rotates the loading structure. I wish to know
> what the rotation parameters mean? Which coordinate sysmtem they
> refere to?
> I check the on-line tutorial. Unfortunately, I didn't get the answer.
>
>   Best
>  Zhong Huantg
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>

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