[Chimera-users] Directly representing ellipsoids

Eric Pettersen pett at cgl.ucsf.edu
Mon Jul 26 22:21:27 PDT 2010

On Jul 25, 2010, at 7:15 PM, Thomas Ouldridge wrote:

> Hi, I'm afraid I'm not a crystallographer/protein simulator, and so  
> this question might seem quite naive. I run coarse-grained  
> simulations, and I would like to represent the objects as ellipses  
> in chimera. I have the position (which I am able to use) and the  
> orientation that I would like my ellipses to take, encoded as a  
> matrix relative to (x,y,z) cartesian coordinates. This matrix gives  
> me the principal axes and radii of the ellipse.
> As I understand, Chimera is designed to display a "Thermal  
> ellipsoid" - I would like this ellipsoid to have the axes and radii  
> given by my matrix. However, it seems that the input (via pdb format  
> files) is interpreted as an "anisotropic temperature factor", and I  
> can't find a way to convert my matrix into the anisotropic  
> temperature factor (I tried some papers online but they seemed to be  
> talking in terms of transformations between lab frame and  
> crystallographic frames, but I cannot see how that applies - what is  
> my crystallographic frame?).
> In short, is there a way to convert my matrix into the "anisotropic  
> temperature factor" representation so that Chimera can read it and  
> convert it back? I did try just plugging in the matrix elements to  
> the PDB file but got some weird ellipsoids out.

Hi Tom,
	The ANISOU record uses the same coordinate frame as the ATOM records,  
so you should be able to just plug in your matrix values.  There are a  
couple of tricks though.  First, the ordering of the six numbers in  
the ANISOU record is (1,1), (2,2), (3,3), (1,2), (1,3), (2,3), i.e.  
first the main diagonal:

(1,1), (2,2), (3,3)

then filling out the first row:

(1,2), (1,3)

then finally the third element of the second row:


Also, the values are integers, and are divided by a factor of 10000 to  
get the final values.
	Is this what you tried?
	It should also be possible to directly assign to the atom's anisoU  
attribute using a Python script if the above doesn't work for some  
reason.  Let me know if you need that.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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