[Chimera-users] Chimera user, about 'turn' command

[Elaine Meng]

On Feb 12, 2008, at 9:35 PM, Aguang Dai wrote:
> I'm a Chimera user in FSU. I would like to use Chimera to build some  
> models.
> I used 'turn' command to rotate the model around the z axis. The  
> command and option was: turn z 27.6923.
> The model is from a PDB file. But the result was that it should have  
> be, not what I wanted.
> The atoms should be always in the circle centered in the Z axis,  
> respectively.
>
> So my question is:
> When Chimera open a PDB file recording a protein structure, whether  
> the coordinate axis is exactly the same as that in the PDB file?
> Thank you for your information in advance.
> Best,
> Daniel

Hi Daniel,
As Tom mentioned, rotation axes are defined relative to the viewer, as  
described here:

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html

and for the input coordinates to match those axes, they must be  
untransformed (not moved after opening, or "reset" to the initial  
position).  Even after resetting, I am not sure whether the center of  
rotation will be where you want it, however, so here are some  
additional suggestions:

(A) you can change the center of rotation.
See the Rotation tool (under Tools... Movement) for how the center is  
calculated and how to change it:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#rotation

(B) you can use a rotation axis defined by the molecule coordinates  
instead of the view, even if you have rotated that molecule (Tools...  
Movement... Constrained Move).  Disadvantages of this tool are that it  
only applies to interactive mouse movement (not with commands like  
"turn"), and when it is turned on, you can only rotate about that one  
axis, so usually one keep turning it on and off to get the position  
you want.

I hope this helps.  If you are still having trouble after trying Tom's  
or my suggestions, please also send the PDB file you are using - that  
would help us understand what you are trying to do.  You could just  
send it to me if you don't want to send to the whole list.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html