Dear cryosparc developpers,
I’ve been using 3DVA extensively and getting beautiful results, thank you very much for this as the results are very interesting.
I want more… I’ve been trying to push 3DVA to larger conformational changes and the results are invariably bad, showing things that clearly are far from the original volume. So I’ve been reading the Punjani&Fleet BioRxiv paper and see that 3DVA assumes a gaussian distribution of particles around the volume and I think it’s where the jobs are failing.
On the grid, I have the whole ensemble of conformations assumed by my transporter, from Inward-facing to outward-facing. I’m able to get high resolution from each conformation, and 3DVA around each volume. I also have “intermediate” particles, that I can’t quite resolve to high resolution, but that I can see belong to some intermediates.
Thus, I’d like to take my million particles englobing all the different conformations, and start a 3DVA job that would give me all the volumes described on the grid, and that would yield all the movements undergone by the protein to go from one conformation to another. Is there a way to do this?
Could it be achieved by giving 3DVA an ensemble of volumes?
Hence the “trajectory” added to 3DVA. If available, this feature would be big hit.