I have two question.
What should be the minimum size for the masking in particle subtraction job?
My model after NU refinement consist of extra region of ~50 kDa which I want to remove through particle subtraction job and want to locally refine rest of the model (150 kDa). But after masking and local refinement, the masked region (50kDa) are still there.
I tried mask tightening and dilation but doesn’t work.
Is there any other method for mask generation different from Segger?
Thanks in advance
To clarify, did you take the consensus structure from NU-refinement and create a mask around the region you wanted to remove, and then use this mask for particle subtraction? This should result in particles where the masked region is gone, but how successful it is will depend on the resolution of density within the mask. Keep in mind that you have to use a mask covering the remaining density for subsequent local refinement jobs (not the mask covering the subtracted density, since it’s already gone from the images). If you’re willing, you could post or DM me some images of the volume in Chimera to show the residual density before and after subtraction.
Yes — in fact we usually recommend using the manual Volume Eraser tool in Chimera to create the mask, because it gives you the most control over selecting the desired region. More info is available on our docs.