[Chimera-users] measure

[Elaine Meng]

Dear Julien,
I believe the command is working in your version.  It does not compare  
the two structures, it only reports how one file has been transformed  
relative to the other in Chimera.  If the coordinates in the two file  
are already rotated relative to each other, Chimera would not detect  
that.  It would report a rotation only if you had moved one model  
relative to the other in Chimera.

If the untransformed coordinates of the two structures are already  
rotated relative to each other, to find out the rotation in Chimera  
you could superimpose them, and THEN use measure to report what  
relative transformation had been employed in the superposition.

I hope this makes sense,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html



On Apr 28, 2009, at 6:31 AM, julien(GWDG) wrote:

> Dear all,
>
> I have the last vesion of chimera 1.4 (27371) under a linux machine.
>
> I want to use the measure function.
> I have two models. The difference between this 2 models is a 5 degree
> rotation around the x axis.
>>> matrix rotation #1 #0
>
>>> reply in the log
> Position of test.pdb (#0) relative to test1.pdb (#1) coordinates:
>  Matrix rotation and translation
>     1.00000000   0.00000000   0.00000000   0.00000000
>     0.00000000   1.00000000   0.00000000   0.00000000
>     0.00000000   0.00000000   1.00000000   0.00000000
>  Axis   0.00000000   0.00000000   1.00000000
>  Axis point   0.00000000   0.00000000   0.00000000
>  Rotation angle (degrees)   0.00000000
>  Shift along axis   0.00000000
>
> I think the command does not work in this version (if I misunderstood
> the command please tell me as well). It always give me the same answer
> for any different models I did try.
> Since I have to ask my admin each time I want to install something,
> could you just tell me in which version of chimera this command will
> work. Many many thanks.
>
> best
>
> Julien
>
> -- 
> European Molecular Biology Laboratory
> Structural and Computational Biology Unit
> Meyerhofstraße 1
> D-69117 Heidelberg
>
> Max-Planck-Institute for Biophysical Chemistry
> NMR based Structural Biology
> Am Fassberg 11
> D-37077 Göttingen
>
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