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

Jian Guan jug25 at psu.edu
Fri Dec 27 10:40:27 PST 2013


Hi Elaine,
Thank you so much for your reply.
I did what you said in the letter. However the return is "Rotation angle is
near zero". Then no axis came out.
What I want to do is to get the elbow angle of the Fab. The elbow angle is
the angle between pseudo 2-fold axes relating heavy and light chains in the
variable domain and heavy and light chains in the constant domain. So I have
to make two axes for variable and constant domain respectively. Then measure
the angles.
Looking forward to your reply.
Thanks,
Jian

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: 2013年12月27日 13:11
To: Jian Guan
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Find pseudo 2-fold axes relating heavy and
light chain

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:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotatio
n>

Ways to superimpose structures are discussed here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> 

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 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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