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@cgl.ucsf.edu] Sent: 2013年12月27日 13:11 To: Jian Guan Cc: chimera-users@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