[scipion-users] 2D masking particles

[Matthews-Palmer, T. <t.m...@im...>]

Dear Scipion Users,

I have a situation where a domain of my object does not align in 2D or 3D (some failed attempts of density subtraction & masked refinement).
I have side-views where this domain is separate (not overlapping) from the rest of the object.
What I would like to do is to apply a fairly tight 2D mask around this domain to the particle images. The xmipp programs in scipion seem to provide a convenient way, however I cannot get it to work right yet.

My workflow is: relion 3D autorefine -> relionc2D without search -> (output classes are therefore oriented as per the 3d map) -> take the side-view class and create a mask -> import mask -> create particle subset from relionc2D of side-view class -> xmipp3 apply 2d mask
The outcome is that the mask is rotated in the output particles, but the transformations are wrong (not even close). If I perform relionc2D without search on the unmasked side-view particle subset, they do not recreate the class average so they must not have the alignments assigned. 

If I do instead:
create particle subset from relionc2D of side-view class -> scipion alignment assign using relion 3D autorefine as input alignments -> xmipp apply 2d mask
Then, checking the particle subset, it can recreate the class average without searching, so it has the alignments, but the mask is not rotated at all in the output particles.

So I tried xmipp3 apply alignment 2d to see if it will actually perform a transformation and interpolation on the particle images and create a new particle stack, but the output particles are unchanged.

Does anyone have experience of 2D masking and have a workflow that works?
Any help greatly appreciated.
All the best,
Teige