Alignment of 3d before using diff map

Hi Jimmy,

I believe the major packages all provide programs for alignment of 3D volumes. For example, Imagic has THREED-ALIGN.

Another solution would be to align the maps manually in Chimera. You would keep the reference map fixed, move the other one until you're happy with the alignment, then use the command vop resample (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html) to resample the aligned map onto the reference map's grid. And then save the aligned map to a new mrc file (Volume viewer>File>Save map as...).

Even if you use a program to do the aligment, you will want to check the result visually (in Chimera perhaps).
Also, if you find that automatic tools do not work well from the starting point, you could do a rough manual alignment in Chimera and then use that as a starting point for further alignment.

Hope this helps,
Alexis