Hi !
I just did a helical symmetry after first helical refine. But the result seems different from the example of cryosparc gui. It doesn’t show specific yellow spot but a yellow area. What does it mean? Is my heterogeneity too high？
Welcome to the forum @mao .
Please can you
- the CryoSPARC version you are using
- the custom parameters specified for the job.
What the sample is would be useful too, as well as not cropping the search range off the plot. The plot would indicate that your helical parameters are a long way off optimal and the search range is insufficient, however amyloids are very difficult to optimise helical parameters for without reaching extremely high resolution (<4 Ang).
If the sample is amyloid, @hickschadw recently shared some extremely useful observations here.
If not amyloid, try refining with helical symmeterisation disabled and use a combination of Chimera (for a rough estimate to start) and the symmetry search tool to try to lock in some potential solutions.
1 Like
Hi wtempel, i’m using the 4.6.2 version. The parameters : pitch 180,220; subunits per turn: 3,6. Others are the same as original.
Do i need increase the range of the plot? I mean the pitch i set was 180,220. Do i need to change to 150,240 or 220,250, like that? There are some amyloids inside the helix but the outside are not.