Hi,
I am trying to sample a PDB with different restraints. I would like to shuffle only some molecules, in order to have some of them in a fixed position (the coordinates should not change after sampling). I define these rigid particles as rigid bodies before shuffling, and suffling as:
IMP.pmi.tools.shuffle_configuration(root_hierarchy, excluded_rigid_bodies=fixed_particles, max_translation=50, verbose=True, cutoff=5.0, niterations=100)
- Fixed particles change their coordinates after shuffling. - In the PDB (4 chains "ABCD"), the chains appear disconnected, even if I apply connectivity restraint.
I may do something wrong, any help would be appreciated!
Thanks!
Altair
On 11/4/20 6:01 AM, Altair Hernández wrote: > I am trying to sample a PDB with different restraints. I would like to > shuffle only some molecules, in order to have some of them in a fixed > position (the coordinates should not change after sampling). I define > these rigid particles as rigid bodies before shuffling
A rigid body is not fixed in space - it is merely constrained to move rigidly. But excluded_rigid_bodies should prevent shuffle_configuration from modifying those rigid bodies. My guess is that your 'fixed_particles' isn't really a list of RigidBody objects and so isn't matching anything. I can't say for sure though without seeing a complete working script.
Ben
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Altair Hernández -
Ben Webb