[Chimera-users] ellipsoid main axis alignment ?

Tom Goddard goddard at sonic.net
Thu Apr 3 15:59:00 PDT 2014

Hi Hugo,

  Chimera has no command for specifying a coordinate system as 3 axes A,B,C.  But you can specify it as a rotation axis and angle that takes the unit vectors (1,0,0), (0,1,0) and (0,0,1) to your A,B,C.  For instance if your A,B,C is a rotation about the z axis by 45 degrees and you want to place an ellipsoid with those primary axes use command

	shape ellipsoid radius 2,3,5 rotation 0,0,1,45 coord #1

The "rotation" argument takes the 3 components of the axis to rotate about and the rotation angle in degrees, and this will be in the coordinate system of already opened model #1.  If the A,B,C vectors are unit vectors then making those the columns of a 3 by 3 matrix produces a rotation matrix and you simply want to use the axis and angle for that rotation matrix.  Of course that requires some computation.  I don't know now you are computing A,B,C but perhaps that code can instead output a rotation axis and angle and you can use the above technique.


On Apr 3, 2014, at 2:45 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Hugo,
> There is a Thermal Ellipsoids tool (and "aniso" command) that shows anisotropic B-factors from the ANISOU records of a PDB file:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/thermal/thermal.html>
> … so one way would be to generate a PDB file with ANISOU records describing your ellipsoids instead of anisotropic B-factors, 
> <http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#ANISOU>
> ...and then read it into Chimera and use this tool.  However, it might be difficult to figure out the correct numbers to put into such records, and also they do not directly specify the size.  The size would be chosen indirectly as a probability level in the Thermal Ellipsoids tool.
> Somebody else may be able to suggest a more direct or efficient way to do what you want.
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Apr 3, 2014, at 11:31 AM, Hugo J Bohorquez <Hugo.J.Bohorquez at FIDIC.org.co> wrote:
>> Hi,
>> I am writing a script in python for generating a series of ellipses linking the nuclei a molecule.
>> Every ellipsoid should be positioned at a specific location P = (X,Y,Z) and should be aligned with the orthonormal vectors describing its main directions-A, B, C.
>> However, when I create an ellipsoid with shape_command it gets located correctly at P but it is aligned with the global axis.
>> I can't find a general way to reorient  an object so its original axes point along the vectors  A, B, and C.
>> I will appreciate any suggestion how to do it.  
>> -- 
>> Hugo J Bohórquez, PhD
>> Investigador
>> Grupo de Biofísica
>> Fundación Instituto de Inmunología de Colombia
>> TEL. +57 +1 -3158920 Ext. 122
>> CEL. +57 315-6169069
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