I got a 4-start helix. The global parameters are twist 40 degree, rise 13.82 Angstrom. How do I define the 4-start helix in parameter for symmetry refinement?
By 4-start, do you mean that the helix has C4 symmetry around the helical axis? If so, then you can input the global parameters (40º, 13.84 Å) as twist and rise, and set symmetry to C4.
If you mean instead that each of the “starts” is offset from each other, translated along the helical axis by the same amount, I believe Shaoda He & Sjors Scheres’s helical reconstruction paper gives an equation to convert the global parameters to ones suitable for refinement. I believe this figure from the paper illustrates this kind of helix.
Oh, I mean the n-start helix with C1. I tried to Shaoda He’s conversion. However, the resolution is decreased not increased. I don’t have this experience so I will play with it a bit more.
Did you try with just the standard params 40º and 13.84Å, and C1 symmetry? I think that would be correct, just would result in less symmetry averaging overall (relative to Shaoda He’s conversion eq.) – but adjacent asymmetric units would still add together coherently as long as each start individually obeys those symmetry parameters.
It actually works very well. So it is my lack of understanding of helical symmetry. 40, 13.84 & C1 I got 5 Angstrom, change to 40 degree, 13.84Angstrom, C4, I got 4 Angstrom and clearly see the side chain.