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View Code? Open in Web Editor NEWIntegrative structure determination of the yeast NPC
Home Page: https://integrativemodeling.org/systems/npc_3.0
Integrative structure determination of the yeast NPC
Home Page: https://integrativemodeling.org/systems/npc_3.0
@iecheverria a number of PDB files look like Modeller outputs, e.g. integrative_structure_modeling/pom152_isolated/data/pom152_E.pdb
. However the Modeller scripts and alignments used to build these models don't appear to be present. Can you add these?
Both IMP sampling scripts fail when running MC:
% cd NPC_3.0/integrative_structure_modeling/pom152_isolated/scripts
% python mod_manual_representation.py
...
Traceback (most recent call last):
File "/home/ben/imp_applications/NPC_3.0/integrative_structure_modeling/pom152_isolated/scripts/mod_manual_representation.py", line 317, in <module>
mc1.execute_macro()
File "/home/ben/imp/release/lib/IMP/pmi/macros.py", line 515, in execute_macro
sampler_mc.optimize(self.vars["monte_carlo_steps"])
File "/home/ben/imp/release/lib/IMP/pmi/samplers.py", line 220, in optimize
self.mc.optimize(nstep * self.get_number_of_movers())
File "/home/ben/imp/release/lib/IMP/__init__.py", line 5619, in optimize
return _IMP_kernel.Optimizer_optimize(self, max_steps)
_IMP_kernel.UsageException: Usage check failure: BallMover can't move non-optimized attribute. particle: Residue_260 attribute: "x"
Context: MonteCarlo0::optimize/MonteCarlo0::do_optimize/SerialMover0::propose/SerialMover0::do_propose/BallMover-Residue_260::propose/BallMover-Residue_260::do_propose
Residue 260 is the first residue in the first rigid body. Looks like you have made every residue in the protein a flexible bead:
for i, mol in enumerate(mols):
dof.create_flexible_beads(mol)
Thus residue 260 has a BallMover but also a RigidBodyMover. That won't work - you can only have one or the other. (I typically see mol.get_non_atomic_residues()
as input to create_flexible_beads
.)
Presumably you fixed this issue for production - can you push the changes to the repo?
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