[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:  
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

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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