hi all, I have a question about how does coot mask the electron density map.
I have a ccp4 electron density map file with parameters like this: Parameters as read from the map file Origin ...................... -167 -36 -35 Extent ...................... 109 74 113 Grid ........................ 156 52 112 Cell axes ................... 100.74 32.81 72.69 Cell angles ................. 90.00 90.71 90.00 UVW (fast, medium, slow) .... Y X Z So this electron density map has 109*74*113=911458 grid points and its origin located at point -167 -36 -35 After I mask part of the density map (around chain B) and only leave electron density around chain A, I export it. Now its parameters are like this: Parameters as read from the map file Origin ...................... 0 0 0 Extent ...................... 156 52 112 Grid ........................ 156 52 112 Cell axes ................... 100.74 32.81 72.69 Cell angles ................. 90.00 90.71 90.00 UVW (fast, medium, slow) .... Y X Z So now the masked map has 156*52*112=908544 grid points with origin locate at point 0 0 0 Before I do tests, I guess how coot to do mask is: to find out grid points around selected atoms from model and set the density value to be zero then save the map like this: 1.1 1.1 2.1 2.1 3.1 --------> 0.0 4.1 4.1 5.1 5.1 So then I can compare the two maps to check out at which point the mask is placed. But actually, the masked map have different points with the initial map. Does anyone know how can I get a masked map with same grid points as the initial map and the only differences are density values at some grid point were set to be zero?
