About 3D variability of membrane proteins

Hi, I have masked out the micelle of a membrane protein I am analyzing, and done 3D variability analysis. I see that the micelle in the output volumes is still there, but it does not move as it should, because it is not considered in the analysis. Is there a way, apart from particle subtraction, not to have the micelle in the output volumes ? I see in the paper of Ali Punjani on the cannabinoid receptor, the micelle in not visible in the output, is it only a matter of threshold ?
Many thanks for your help !

also another question from reading Ali’s paper. When it says:
we display renderings of the 3D density generated
by the linear subspace model at negative (red) and positive (blue) values of the reaction coordinate for individual variability components. @apunjani the output from 3D variability display in simple mode, has 20 frames for each component. could you explain me if possible, which frames do you choose as negative (red) and positive (blue) ? Are these the first and last frame, for example ? Or you refer to a different output of the variability display ? Many thanks and sorry if I have missed this info somewhere else

Hi @marino-j ,

Regarding the micelle, in the paper results yes we just were able to threshold it out in chimera for visualization.
As you said, particle subtraction would be the only way to reduce the micelle density in the output of 3DVA. We have to keep the micelle in the consensus density (V_0 in the paper) because it is really there in the images.

For the red/blue plots, we just used the 2nd and 19th volume from the series generated.

Hope that helps!

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Thank you, @apunjani. Very helpful !