IMP  2.3.1
The Integrative Modeling Platform
atom/markers.py

It is often useful to be able to add extra particles to a model to act as markers for particular features. Examples include creating a bounding sphere for some part of a molecule and using the bounding sphere particle in a distance restraint. The IMP.atom.create_cover() is such a function, creating a particle whose IMP.core.XYZR sphere contains the passed IMP.atom.Selection at all times.

The same code also works (more efficiently in fact) if the protein is made into a rigid body.

1 ## \example atom/markers.py
2 # It is often useful to be able to add extra particles to a model to act as markers for particular features. Examples include creating a bounding sphere for some part of a molecule and using the bounding sphere particle in a distance restraint. The IMP.atom.create_cover() is such a function, creating a particle whose IMP.core.XYZR sphere contains the passed IMP.atom.Selection at all times.
3 #
4 # The same code also works (more efficiently in fact) if the protein is made into a rigid body.
5 #
6 
7 import IMP.atom
8 import IMP.display
9 
10 m = IMP.kernel.Model()
11 h = IMP.atom.read_pdb(IMP.atom.get_example_path("example_protein.pdb"),
12  m)
13 # residues 100 and 153 are two residues that are close together
14 # spatially, create a marker for the volume around them
15 s = IMP.atom.Selection(h, residue_indexes=[100, 153])
16 marker = IMP.atom.create_cover(s, "my marker")
17 m.update()
18 
19 # if we now move the protein, marker will move along with it
22 IMP.atom.transform(h, tr)
23 m.update()
24 
25 # display it to a file
26 w = IMP.display.PymolWriter("marker.pym")
27 g = IMP.core.XYZRGeometry(marker)
28 g.set_color(IMP.display.Color(0, 1, 0))
31 gs.set_color(IMP.display.Color(1, 0, 0))
32 w.add_geometry(g)
33 w.add_geometry(gp)
34 w.add_geometry(gs)