Mode 4
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During a recent project, I plotted the particles' euler angles before and after a few rounds of mode 4, DANG 20, ITMAX 200 (frealign_v9.11). Attached you can see that a small portion of the particles now line up along the meridian of each of the graphs. More rounds of mode 4 or refining through mode 2 and 1 do not remove this feature. Could this be from some preferred orientation of the particle in ice or am I assaying too many orientations with mode 4 at such a fine angular step? Has anybody seen this before?
I think it would be better to
I think it would be better to use Mode 3 for initial angle assignment. Choose a search angle (DANG) of 5 deg. This has worked quite well for many projects.
Mode 3 with 5 degree
In reply to I think it would be better to by niko
Mode 3 with 5 degree increments works well in my case. No more meridian effect. Thanks, Niko.
Interestingly, the average particle score improved similarly when using either mode 3 or 4, as did the resolution achieved. I suspect that the low contrast of some of my particles may make them difficult to align.