[Chimera-users] ellipsoid main axis alignment ?

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 3 14:45:39 PDT 2014


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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