On 04/11/2016 15:55, Tim Gruene wrote:
I would like to draw the surface of a (small) molecule, e.g. at VdW-radius, and display by colour the map values from an mtz-file at the surface.
There is no interface to do this.
Ideally I would like to set surface distance from the nuclei, the central, maximum, and minimum level for the colouring. Is this possible with Coot?
The code for the vdW surface of residues/ligands doesn't explicitly export the point positions - but it would be easy to add (or for you to do it if you compile from source code). You can then easily get the map value using density_at_point(). Then you'd have to map the density value to a colour and then display the point (to_generic_object_add_point()).
It would be nicer to export these points and colours and display little transparent coloured discs perpendicular to the nearest atom. Maybe pyMOL can do that. It would be doubly cute to have an animation of these disks as you vary the a multiplier of the vdW radius (say from 2.0 to 0.2).
Paul.
