[Chimera-users] saving with angles

Thomas Goddard goddard at cgl.ucsf.edu
Tue Dec 12 09:39:38 PST 2006

Hi Gabor,

  Thanks for the details about what you are doing.

  The Fit Map in Map tool I gave you reports the 3 by 3 rotation matrix and
the translation vector to fit one map in another in the Chimera Reply Log
which is displayed with menu entry Favorites / Reply Log.  Here is an
example of the output:

Fit map microtubule.mrc <1> in map microtubule.mrc using 11355 points
  correlation = 0.999, overlap = 3.167e+08
  steps = 68, shift = 7.29, angle = 5.69 degrees
Transformation of microtubule.mrc <1> (#1) in microtubule.mrc (#0):
    0.99999980  -0.00061658   0.00010850  -0.06294723
    0.00061658   0.99999981  -0.00002551  -0.03578213
   -0.00010849   0.00002558   0.99999999  81.17044268

In this example I just fit a microtubule map to itself shifted along
its length.  The rotation matrix is the first 3 columns and you see it
is approximately the identity matrix.  The shift is the last column,
81 angstroms along the z-axis.  The third line that reports "shift"
and "angle" just indicate how big a move was made from the hand-placed
position to the optimal fit -- not the relative orientations of the maps.

  I don't know if this matrix is usable in IMAGIC.  I could easily add
the same information in expressed as rotation axis vector and rotation
angle.  Euler angles is a bit trickier since there are many alternate

  By the way, I changed the way correlation is calculated to use the
conventional meaning.  It is described in the Chimera manual.


The code I gave you gave higher correlation values using a different
definition.  The code optimizes overlap, not correlation, so the actual
fitting has not changed.  I also added an option to only use the data
within the contour surface for fitting.  The new code is on the web
and should work with Chimera 1.2309


  Michael Schmid at Baylor College of Medicine gave an interesting talk
on aligning tomograms of carboxysomes in a way that accounts for the
missing wedge.  I think this paper reports the results (I have not read it).

    Schmid MF, Paredes AM, Khant HA, Soyer F, Aldrich HC, Chiu W, Shively JM.
    Structure of Halothiobacillus neapolitanus Carboxysomes by Cryo-electron Tomography.
    J Mol Biol. 2006 Dec 1;364(3):526-35. Epub 2006 Sep 14. 


  I leave today for a workshop in Germany and return Sunday.  So I will
not be able to offer more help until Monday.


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