Hi Weimin, As Giovanni pointed out, use the mask command "fullmap true" option to avoid getting a smaller masked map. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html The reason your contour surfaces don't look good after masking when the contour level is set to the same or a close value to that used for masking is because the data was set to zero below that contour level. The contour surface points are calculated by tri-linear interpolating between grid points where data values are higher than the threshold, and adjacent grid points that are lower than the threshold level. If you set those lower values all to zero the interpolation gives a much nastier looking surface with many staircase artifacts because you many different smoothly varying values below the threshold all to the same much lower value, namely zero. To avoid this you should mask at a much lower threshold so the neighbor grid points just out side the contour levels you really wish to display are not set to zero. The hide dust tool doesn't show these artifacts because it doesn't change the map data, it merely undisplays small surface blobs. Tom

Sometimes after we remove the dust using the tool of hiding dust, we want to save the map directly instead of using command "mask #0 #0" to generate a maskfile. The reason is that the masked map has minimized map size and different with original one. Even after we recover the map size and origin, it always has half pixel issue, and if we apply this mask to original map, the output will have some masking artifact. The iso-surface of the output will not be as smooth as original map or the map after hiding dust.

weimin