On 20/03/19 19:49, Ahmad Khalifa wrote: > I have a cryo-EM map that I want to segment.
"segment" as in what segger does? Or merely create a masked map? > I have structures surrounding the density of interest from all sides. > I used chimera to subtract everything and clean the density using > volume eraser. OK, you can do that in coot too (if I understand what you did). > > The screenshot is what I got: > > 1) the structure is not fitted No... So I see. Generally one puts the molecule in the centre of the cube of the reconstruction and fits a molecule there. So I suggest you do that (reading in the map into a fresh coot session will do that). Then read in your molecule model. Then use Calculate -> Move Molecule Here. Turn on the unit cell to help you out. maybe a bit of jiggle-fit will help? > 2) the density appears to have multiple copies of my proteins, it's > supposed to be only one there! Coot doesn't yet know not to draw density outside the box when it has a cryo-EM map. > > What is wrong here exactly, I'm suspecting it's the volume eraser! Maybe... but I doubt it. It's easy to apply transformations to maps and models in chimera (and not really know it?). That's much harder to do in Coot. > Is there a better way to segment the density given how I have atomic > models for all the surrounding densities, but not the density of > interest? > What would be the result of segmentation? You model looks like it would fit your map. Paul. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
