Hi @vincent, thanks for the clarification - I was not aware of the structural difference between belts and micelles so this is very helpful. Thanks!
@fernandesj, for 3D Variability you should create a mask that includes (i.e. has value 1.0) the part of the structure you want to consider during 3DVA processing, and value 0.0 for parts to exclude (ideally with a soft falloff in between). You can create this in the simplest case by
- opening your current refined density map (the
map, notmap_sharpoutput) in Chimera, and noting the threshold at which only the desired part of the structure (maybe only protein, excluding the detergent) is visible. - create a “volume tools” job in cryosparc and connect the refined map as as input. Set “type of output volume” to mask, and set “Threshold” to the threshold from Chimera. Then set the “Dilation radius” and “Soft padding width” to a distance in pixels that will define how much the selected density is dilated and softly padded to create the final mask. Once this job runs, you can download the mask and open in Chimera with your density map to verify that it includes the correct regions
- Connect the mask output from Volume Tools to your 3DVA job.