Hi,
I have an issue that expands on this post: Flipping hand causes strange issues
I have a case where I’ve tried both 1. flipping my latest 3D reconstruction with Vol Tools and refining my particles into that volume, and 2. Heterogeneous Reconstruction Only with flipping turned on, and both methods cause artifacts. I believe I did the 2nd method correctly, which mmclean describes in the thread above, the only difference for my dataset is that I have no symmetry, so I skipped the Volume Alignment Tools step listed.
Here’s a comparison of volumes from what I tried using the 2nd method:
Volume 2 looks like it correctly flipped the volume/particles, but when I use those particles in subsequent jobs (Volume 3) there are artifacts.
This is a challenging dataset of a small, ~100 kDa, Fab-antigen complex. I’ve employed the very extensive ab-initio parameters (0.005 Fourier radius step, etc.) for small molecules to arrive at this reconstruction. I definitely want to use these particles for subsequent jobs, in the correct handedness, but am afraid of any artifacts/misalignments.
Thanks for your time,
David