Search mode 4 parameters
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Hello,
In mode 4 we can set the angular step size for the systematic search with DANG, and the number of starting angles to be tested with ITMAX.
In your hands, what is the most successful combination? ITMAX 100, DANG 100, as in your 2007 jsb paper? Or some other variations of the two? (I was thinking about trying DANG 15, ITMAX 25)
Also, should we use different strategies for symmetric and asymmetric particles?
Many thanks,
The success of the search
The success of the search strategy depends on your data. It is usually a good idea to run a search for a 100 typical particles and then check the matching projections to make sure the correct orientations are found. You should try different strategies to find the best one.
A search is very slow, however, and orientations might not be found correctly. It is usually much better to try and convert the angles that you found with Spider or IMAGIC (or whatever program you used before starting with Frealign). The Spider angles should be the same as the Ffrealign angles. For IMAGIC, there is now a command built into the latest version of IMAGIC that does the angle and shift conversion into Frealign.