Dear cryoSPARC community,
I’ve been using the 3DVA to look at the motion of a small protein (about 150 kDa). The protein has three domains, and I know that one domain is quite flexible, but it was still possible to resolve it. In 3DVA this specific domain tends to disappear during the motion. It doesn’t disappear completely, but I’d say about half of it does. So, I’m wondering how can I interpret this? Am I doing something wrong or is this effect an indication of the high flexibility of this domain? I’ve ran 3DVA in simple mode with 10 components as output and I tried 3.5, 5 and 8 A filter (the protein is resolved at 3 A). I noticed this domain “disappearing” independently from the filter value, and it occurs in the first few components.
Thank you all for your help!
Lavinia