[Chimera-users] Chimera rotational matrix

[Thomas Goddard]

Hi Huy,

   To add a bit to what Elaine and Greg said, here is the command to 
rotate map #0 about its local z axis with the center specified in map 
coordinates (physical units using volume voxel size and origin, not grid 
indices):

	turn z 30 center 0,0,0 coord #0

And if you have other models open but only want to rotate map #0 then 
you can use

	turn z 30 center 0,0,0 coord #0 model #0

These extra options to the "turn" command are only available in the 
Chimera 1.4 daily builds.

	http://www.cgl.ucsf.edu/chimera/alpha-downloads.html

Here's the new documentation for "turn":

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

   Tom



Elaine Meng wrote:
> Hi Huy,
> Just to add to what Greg said:
> In recent builds of Chimera, the movement commands (roll etc.) have  
> been improved so that you can specify the center of rotation to use in  
> that movement, without changing the Chimera interactive center of  
> rotation.
> 
> For example,
> 
> roll z -30 1 center 0,0,0
> 
> will use 0,0,0 in the "laboratory" frame of reference as the rotation  
> center for the roll.  You can also specify a center in the coordinate  
> system (frame of reference) of any of the models instead of the  
> laboratory frame of reference.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/roll.html>
> 
> The transformation matrix can be shown in the Reply Log with the  
> command:
> 
> matrixget -
> 
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html>
> If you didn't do any other movements and then used the roll command  
> above, the translation vector in the fourth column of the matrix would  
> contain zeros.
> 
> The improved movement commands are available in recent daily builds:
> <http://www.cgl.ucsf.edu/chimera/alpha-downloads.html>
> 
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> 
> On Nov 30, 2008, at 9:45 PM, Greg Couch wrote:
> 
>> On Thu, 27 Nov 2008, Bui  Khanh Huy wrote:
>>
>>> Hi,
>>> I notice that Chimera has slightly different in calculation of  
>>> transform
>>> when I tried to rotate my EM density (200x200x200 mrc file) using
>>> Chimera. The origin of the density reported by Volume Viewer is 0,0,0
>>>
>>> First, I print out the homologous transform matrix using:
>>>
>>>>>> om = chimera.openModels
>>>>>> mlist = om.list()
>>>>>> m = mlist[0]
>>>>>> print m.openState.xform
>>> The transformation is:
>>>
>>> 1 0 0 0
>>> 0 1 0 0
>>> 0 0 1 0
>>>
>>> If I rotate the model using command:
>>>
>>> roll z -30 1
>>>
>>> Then print out the transform matrix again:
>>>
>>> 0.866025 0.5 0 -36.8852
>>> -0.5 0.866025 0 61.2937
>>> 0 0  0 1
>>>
>>> That would be weird because I didn't do any translation.
>>> So what is really happening in Chimera when I rotate the model?
>>> Best,
>>> Huy
>> The model is rotated about its center.  So unless your model is
>> centered at the origin there will be a translation component.  If the
>> rotation is R, and T is the translation to the center, then the actual
>> rotation is:
>>
>> 	R' = T R (-T)
>>
>> Chimera has many different ways to choose the center.  See
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#rotation 
>> for details.
>>
>> 	Greg Couch
>> 	UCSF Computer Graphics Lab
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