Greetings, I’m looking for some advice on how to optimize my 3D Flex training, if possible.
Backstory:
I have a ~150 kDa protein complex and the main, ~120 kDa region resolved to ~2.7 angstrom. But the hard part to refine has been this accessory domain; its only 22 kDa and connected by two very flexible linkers. 3D classification from my initial 1.5 million good particles gets this domain to maybe 8 angstrom. So I’ve been trying to sort out if I could improve this with 3D Flex refinement. For now I am using 10% of my particles, as a test case to speed things up.
Question part:
After making a custom mesh from my segment map (I kept the main domain rigid), I ran flex training with 2 latent dimensions and am still fine-tuning latent centering strength. My current best map still shows a ton of smearing, however. Some questions I have are:
- How can I tell if I need to increase the number of latent dimensions?
- Should I be worried that my full/rigid validation don’t diverge?
- Am I delusional for trying to refine something this small and this flexible to begin with?
Thank you,
Kevin