[Chimera-users] Find pseudo 2-fold axes relating heavy and light chain

Elaine Meng meng at cgl.ucsf.edu
Fri Dec 27 10:11:08 PST 2013

Hi Jian,
Define Axes creates a best-fit axis to the atoms you specify.  It is not meant to find axes of symmetry or pseudosymmetry.

I would recommend opening two copies of your structure, then superimposing them based on the parts that are pseudosymmetric (the parts that are pseudoequivalent), then using command "measure rotation" with option "showAxis true" (or maybe "showSlabs true") to show the axis of rotation between the two copies:

Ways to superimpose structures are discussed here:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 27, 2013, at 8:08 AM, Jian Guan wrote:

> Dear all,
> I am trying to find pseudo 2-fold axes relating heavy and light chains in
> the constant domain and variable domain respectively in Fab.
> I tried Define Axes, it failed. 
> And I made artificial double heavy chain, it failed again. I can only get
> axis which is horizontal passing through both light chain and heavy chain.
> It is not what I want. 
> Can anyone help to give some clues?
> Thanks
> Jian

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