reliontomo: 3d classification --flatten_solvent parameter

[plosana]

the parameter flatten_solvent, which limits the size of the initial model, is hardcoded on the parameter of 3d classification, and is passed through even when no mask is provided.
This provokes that the final volume is smaller than expected:

Please set it to True only when a mask is provided to avoid unexpected outputs

[pconesa]

Thanks Patri. @JorMaister will you take care of this too?

[JorMaister]

Hi @plosana,
We're passing the --flatten_solvent argument following the source 3d classification command composition. Hence, the problem reported regarding the size may be originated from other reasons. Below there's a screenshot of the code mentioned:

[azazellochg]

from Sjors in 2014: "If you do not provide this option, the reconstructions will not be masked other than a spherical mask with the diameter being the size of the box. If you do provide this option it will either use a spherical mask with the diameter as given on the General tab (which is probably smaller than the box size), OR a user-specified mask if you give one in the Reference mask option below on the Optimisatiojn tab." - might have changed since

[JorMaister]

That's quite clarifying, @azazellochg. many thanks!

Thus, considering that the --flaten_solvent is expected to be always active in the current code, the small size behavior observed can be controlled via the box size or the mask, depending on the combination. That's good to know. I suppose it manages the presence or not of the mask internally as in the command composition the mask only appears as shown in the image below, and those code lines are right below the ones attached in my previous comment.

[pconesa]

So, does this mean that is an option we should expose in the form?

[azazellochg]

in relion plugin it's an option with default=True

[pconesa]

Let's make it a param just ins case and forget about this. Default to true.