Hi @lorago92 ,
Thanks for re-running this – the FSCs are looking more accurate now, in the sense that you can tell that the unmasked (and spherically and loose masked) FSCs are reasonable for the resolution of the current model. The issue now is that the tight mask is too tight, and inflates the resolution estimate. You may find this previous forum post useful.
We’re aware that the FSC masking parameters (that control the “tightness” of the masks) could be better tuned for lower resolution datasets in the sub 6Å range, and are considering the best way which we can remedy this issue. Unfortunately, as of now these parameters are not accessible in most refinement jobs. The best workaround to this problem is as follows:
- Launch a Volume Tools job to manually create a mask around your structure via thresholding and padding (recommended that the soft padding width follows our rule of thumb)
- (If enforcing helical symmetry): Take your particles and volume from the Helical Refinement and optionally run symmetry expansion if the correct helical symmetry parameters are known
- Take the expanded particles, generated mask from Volume Tools, and density map from Helical Refinement, and connect these to a Local Refinement job for further processing
Local refinement uses the input mask for all FSC estimation, which works-around the issue of overly tight FSC mask parameters.
I hope this helps,
Michael