search

timothygrant80 / cisTEM

Other
32 stars 27 forks source link

Circular masks on half-maps #519

Open jojoelfe opened 1 month ago

jojoelfe commented 1 month ago

The EMDB is now requesting that the deposited half-maps have no masking applied to them:

https://www.ebi.ac.uk/emdb/documentation/policies#3-1-1

But, reconstruct3d applies spherical masks on the half-maps before saving them:

https://github.com/timothygrant80/cisTEM/blob/64a125a7fef92f0aa84ad28ff0980b133a125d61/src/core/reconstructed_volume.cpp#L617-L624

We probably should give at least an option to not do this, I'm just not sure whether this will be an issue during refinements. @bHimes @timothygrant80 any idea what would be best?

timothygrant80 commented 1 month ago

I think it would be fine to just write it out unmasked. When i need half maps for EMDB, I just run Generate3D with save half maps set to yes, and the mask radius to a very large number, but it would be fine to basically always write out the half maps as unmasked.