Helical Tutorial Symmetry Output

Troubleshooting
1

Hi All,

I’m going through the tutorial for helical processing and I’m having an issue with the symmetry search step. The tutorial says I should see

Showing the 20 best local minima.
No. | p (A) | n | dz (A) | dphi (deg) | mse

00 | 018.059 | 003.549 | 005.088 | +101.436 | 1216.663

But my output is different

Showing the 20 best local minima.

[CPU: 749.3 MB] No. | p (A) | n | dz (A) | dphi (deg) | mse

[CPU: 749.3 MB] -------------------------------------------------------------------------

[CPU: 749.3 MB] 0 | 4.259e+01 | 3.020e+00 | 1.410e+01 | -1.192e+02 | 2.247e+03

[CPU: 749.3 MB] 1 | 4.929e+01 | 3.706e+00 | 1.330e+01 | -9.714e+01 | 2.370e+03

[CPU: 749.3 MB] 2 | 4.488e+01 | 3.431e+00 | 1.308e+01 | -1.049e+02 | 2.437e+03

[CPU: 749.3 MB] 3 | 4.435e+01 | 3.412e+00 | 1.300e+01 | -1.055e+02 | 2.438e+03

[CPU: 749.3 MB] 4 | 4.118e+01 | 3.255e+00 | 1.265e+01 | -1.106e+02 | 2.498e+03

[CPU: 749.3 MB] 5 | 3.659e+01 | 3.392e+00 | 1.079e+01 | -1.061e+02 | 2.620e+03

[CPU: 749.3 MB] 6 | 4.241e+01 | 3.686e+00 | 1.151e+01 | -9.766e+01 | 2.649e+03

[CPU: 749.3 MB] 7 | 3.253e+01 | 3.294e+00 | 9.875e+00 | -1.093e+02 | 2.663e+03

[CPU: 749.3 MB] 8 | 3.835e+01 | 3.922e+00 | 9.780e+00 | -9.180e+01 | 2.665e+03

[CPU: 749.3 MB] 9 | 3.200e+01 | 3.275e+00 | 9.772e+00 | -1.099e+02 | 2.665e+03

[CPU: 749.3 MB] 10 | 3.006e+01 | 3.216e+00 | 9.348e+00 | -1.120e+02 | 2.691e+03

[CPU: 749.3 MB] 11 | 3.341e+01 | 3.157e+00 | 1.058e+01 | -1.140e+02 | 2.705e+03

[CPU: 749.3 MB] 12 | 4.576e+01 | 4.569e+00 | 1.002e+01 | -7.880e+01 | 2.712e+03

[CPU: 749.3 MB] 13 | 4.700e+01 | 4.608e+00 | 1.020e+01 | -7.813e+01 | 2.713e+03

[CPU: 749.3 MB] 14 | 3.271e+01 | 6.686e+00 | 4.891e+00 | -5.384e+01 | 2.764e+03

[CPU: 749.3 MB] 15 | 1.753e+01 | 3.471e+00 | 5.051e+00 | -1.037e+02 | 2.771e+03

[CPU: 749.3 MB] 16 | 1.859e+01 | 4.392e+00 | 4.232e+00 | -8.196e+01 | 2.812e+03

[CPU: 749.3 MB] 17 | 1.894e+01 | 5.961e+00 | 3.178e+00 | -6.039e+01 | 2.818e+03

[CPU: 749.3 MB] 18 | 2.600e+01 | 5.431e+00 | 4.787e+00 | -6.628e+01 | 2.826e+03

[CPU: 749.3 MB] 19 | 1.400e+01 | 3.098e+00 | 4.519e+00 | -1.162e+02 | 2.826e+03

[CPU: 749.3 MB] -------------------------------------------------------------------------

[CPU: 753.5 MB] Done in 14.468s.

[CPU: 443.9 MB] --------------------------------------------------------------

I’ve followed all the steps in the tutorial, and if I put in the values of symmetry from the tutorial my map looks really nice, but I’m not sure if I’m not reading my table correctly or if there is a global config or something that I’m missing. Thanks for any assistance.

Bryan

2

Hey @hansenbry,

Due to the ambiguities in helical symmetry that are inherent in the way projection images are formed, it can happen that the asymmetric refinement doesn’t converge to a solution for the symmetry parameters, and thus the correct solution doesn’t show up as the global optima in the table printed out (or even that the wrong solution is converged to). Unfortunately, this is why asymmetric refinements and ab-initio reconstructions with helical symmetry are not guaranteed to lock on to the right symmetry, and it can depend on the dataset and initialization. We still chose to illustrate a workflow in the tutorial where asymmetric refinements/ab-initio reconstructions can work, because for many datasets this is a viable workflow (especially filaments with large asymmetric units, like EMPIAR-10495 and EMPIAR-10213). There’s a bit more of a discussion on this phenomenon in the Helical ambiguities post, and on Prof. Egelman’s paper on the subject.

In your case, it looks like the 15th row is fairly close to the true solution, with a rise of 5.051 Å and twist of -103.7º. You could try doing a second refinement with these symmetry parameters, which are a lot closer to the true optimum.
15 | 1.753e+01 | 3.471e+00 | 5.051e+00 | -1.037e+02 | 2.771e+03

Best,
Michael

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