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: https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=experimental/fitmap2318... The zip file contains a directory FitMap that you put in your Chimera distribution under chimera/share or on Mac Chimera.app/Contents/Resources/share For more installation details see http://www.cgl.ucsf.edu/chimera/experimental/install.html 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: http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001313.html 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). Tom 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