Hi,
I am trying the helical refinement introduced in V3. Is there a way to find the final twist and rise of the refine structure?
Thanks
Hi @bcanax,
If local searching of the helical twist and rise is enabled, then a plot that looks like the following will be displayed in the streamlog at each iteration, along with the optimal twist/rise at that iteration. The plot will be the last in the series of plots made at each iteration. The plot shows the error function over various symmetry parameter combinations: for example, in the image below, it shows that the optimal twist is 29.422 degrees and optimal rise is 21.794 Angstroms.
If you aren’t seeing this plot, that means that the twist and rise aren’t being optimized at that iteration. You can control when the searching is done by changing the “Resolution to begin local searches of helical symmetry” parameter. By default, this parameter is set to 5 Å, meaning that the twist and rise will be optimized only if your structure reaches 5 Å or below. If this is too high of a resolution, you can increase this to 6-8 Å. Generally, values under 8 Å are recommended, as the searching may converge to incorrect values when the structure is too low resolution – but it certainly depends on the dataset.
Let me know if you have any other questions!
Best,
Michael