specifying parameters for helical symmetry
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I have some problems how to give parameters to impose helical symmetries in Frealign
Readme says: " #SUBUNITS = #STARTS x D / RISE" My interpretation is that #STARTS then is a function of the overlapping in segment picking and that 90% overlap gives #STARTS=0.1. On the other hand "The number of starts in the helix" would be 10. When I use 0.1 I get reasonable results but in the resulting parameter file I get "C Number of starts . . . . . . . . . 1".
Thankful for any clarifications/Martin
Did you check the example for
Did you check the example for TMV that is included with the distribution? For TMV (also 90% overlap), the values are
Step size D = 70 Angstroms (from our 2007 TMV paper)
RISE = 1.408 Angstroms
#STARTS = 1
#SUBUNITS = 1 * 70 / 1.408 = 49.7
In the example that comes with the distribution, we set #SUBUNITS = 49. The value for #SUBUNITS does not need to follow exactly the formula given in the README file. It is just a guideline to tell Frealign how much averaging it should do.