[Chimera-users] translation matrix

Tom Goddard goddard at sonic.net
Mon Dec 2 10:05:41 PST 2013

Hi Antón,

  The "measure rotation" command gives the rotation and translation in the Reply Log dialog (menu Favorites / Reply Log).  It only reports the rotation angle in the status line at the bottom of the main window.  Keep in mind that "measure rotation #0 #1" measures the difference between the coordinate systems for the two models.  If you simply open any two PDB models and use measure rotation it will give zero rotation and translation because they start out with the same coordinate systems.  If you use Match Maker or the match command it will move the coordinate system of one model relative to the other to achieve the alignment and then measure rotation will give a non-zero rotation and translation.


On Dec 2, 2013, at 7:37 AM, Antón Vila Sanjurjo  wrote:

> Hi, 
> I'm trying to get a translation matrix for two different crystal structures of ribisomal subunits. I've been trying to use the "measure rotation" command but I can only get it to display the following message "rotation angle is near zero (0 degrees)". I was wondering whether the command might be failing due to the fact that the ribosome contains numerous chains, or perhaps because the command does not deal with RNA. At any rate, how would one go about obtaining a translation matrix that can be applied to any model?
> best,
> Antón
> -- 
> Antón Vila-Sanjurjo, PhD
> Marie Curie fellow
> Grupo QOSBIOS, Dept. Química Fundamental
> Facultade de Ciencias
> Universidade de A Coruña (UDC)
> Campus Zapateira, s/n
> 15.071 - A Coruña - España (Spain).
> tlf: (34) 981-167000 ext:2659
> e-mail: antonvila.s at gmail.com
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