We are interested in integrating the 3DFlex pipeline inside Scipion, including the ability to interactively generate different conformations from the latent space learned by 3DFlex.
However, we are unsure about the appropriate way to call 3DFlex from the command line to generate a given conformation from a specific set of latent space coordinates. If this capability is already implemented in CryoSPARC, what would be the appropriate way to call 3DFlex for this purpose? Is there any other way to generate specific conformational states from the network?
Thank you in advance for your help, and I look forward to your response.
I think cryosparc-tools would be the easiest way to generate maps from arbitrary latent space coordinates. You could use code similar to that in this example (perhaps providing the pts array manually rather than clicking a plot) to generate the latent coordinates.
You could then use cryosparc-tools to programatically create a 3D Flex Generate job and connect the latent coordinates output to the generate job’s input. An example of programmatic job creation and connection is available in this example, among other places.
This was exactly what we were trying to find to execute 3DFlex with custom latent vectors, thank you so much for your answer and for the examples they have been very helpful!