[Chimera-users] Map Orientation for Symmetry Plug-in

Tom Goddard goddard at cgl.ucsf.edu
Tue Feb 6 16:02:58 PST 2007

Hi Albion,

  Ok, I made the "fit map in map" tool print out a point on the rotation 
axis.  The new code for use with Chimera 1.2318 is here:


The zip file contains a directory FitMap that you put in your Chimera 
distribution under


or on Mac


For more installation details see


This FitMap directory replaces your existing one.

  After restarting Chimera you can fit a helically symmetric map in a 
rotated copy of itself then get the axis point (shown in Favorites / 
Reply Log) and adjust the map origin (volume dialog Features / Origin 
and Scale) to put the axis point at (0,0,0).  I described this in more 
detail in my previous message:


The output of the axis point will be included in the next Chimera 
snapshot due out in one to three weeks.

  The matrix you sent me had no rotation, just a translation by 52 along 
z.  You will need to rotate the map copy before fitting to get a 
meaningful rotation axis point.  In fact I suspect the accuracy will be 
increased for rotations near 180 degrees rather than small rotations 
(e.g. 30 degrees).


Albion Baucom wrote:
> Thanks Tom.
> OK, here is my rotation matrix after following your instructions
>     0.99944468  -0.03326699   0.00190528  -0.09024247
>     0.03326443   0.99944566   0.00136109   0.10539160
>    -0.00194951  -0.00129696   0.99999726  52.82194789
> Sorry, I forgot how to compute the rotation axis vector from this 
> matrix ... its been awhile since I had to do that manually ... its 
> pretty simple if I remember right.
> Any code to automate this would be greatly appreciated.
> Thanks again!
> Albion

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