6.17 Masks

A map can be masked by a set of coordinates. Use the scripting function:

(mask-map-by-molecule imol-map imol-model invert-mask?)

If invert-mask? is 0, this will create a new map that has density only where there are no (close) coordinates. If invert-mask? is 1 then the map density values will be set to zero everywhere except close to the atoms of molecule number imol-model.

The radius of the mask around each atom is 2.0Å by default. You can change this using:

(set-map-mask-atom-radius radius)

There is a GUI interface to Map Masking under the Extensions menu.

6.17.1 Example

If one wanted to show just the density around a ligand:

1. Make a pdb file the contains just the ligand and read it in to Coot - let's say it is molecule 1 and the ligand is residue 3 of chain “L”.
2. Get a map that covers the ligand (e.g. from refmac). Let's say this map is molecule number 2.
3. Mask the map:

   (mask-map-by-molecule 2 1 1)

   This creates a new map. Turn the other maps off, leaving only the masked map.

To get a nice rendered image, press F8 (see Section Raster3D).