IMP  2.3.0
The Integrative Modeling Platform
collision_cross_section.py
1 ## \example em2d/collision_cross_section.py
2 # Example of how to compute the collision cross section of a molecule.
3 #
4 
5 
6 import IMP
7 import IMP.em2d as em2d
8 import IMP.atom as atom
9 
10 """
11 
12 Example of how to compute the collision cross section of a molecule
13 
14 """
15 
16 
17 IMP.base.set_log_level(IMP.base.TERSE)
18 m = IMP.kernel.Model()
19 
20 fn = em2d.get_example_path("1z5s.pdb")
21 prot = atom.read_pdb(fn, m, atom.ATOMPDBSelector())
22 atom.add_radii(prot)
23 
24 
25 projections = 20
26 resolution = 1.0
27 pixel_size = 1.5
28 img_size = 80
29 ccs = em2d.CollisionCrossSection(projections, resolution, pixel_size, img_size)
30 ccs.set_model_particles(IMP.atom.get_leaves(prot))
31 print "CCS", ccs.get_ccs(), "A**2"
IMP::em2d
Restraints using electron microscopy 2D images (class averages).
IMP::base::set_log_level
void set_log_level(LogLevel l)
Set the current global log level.
IMP::atom
Functionality for loading, creating, manipulating and scoring atomic structures.
IMP::atom::get_leaves
Hierarchies get_leaves(const Selection &h)
IMP::kernel::Model
Class for storing model, its restraints, constraints, and particles.
Definition: kernel/Model.h:73