Yes, Paul's analysis of the problem is correct.
Coot is the wrong tool for this job. You can do the job in CCP4 using
NCSMASK and MAPMASK.
Open Map & Mask Utilities.
Use Create/Edit Mask to make a mask about your model. Enter the grid and
extent values from your current map. Use a pdb file containing only
chain B. Turn off the 'trim mask' option.
Use Edit/Rotate maps and masks and select 'solvent flatten a map using a
mask' to flatten the unmasked region.
Kevin
[email protected] wrote:
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?
