8. xl2 is set up with a distance threshold of 35 A ˚ . This distance is
derived from the BS3 cross-linker molecule length (11 A ˚ ), two
lysine side chains (2 Â 7 A ˚ ) and an additional 10 A ˚ which
permits small-scale subunit translations and rotations and prevents the system from being locked into a particular
conformation.
9. The EM restraint is set by lines 171–178. In the first step, a
GMM map is calculated for each subunit. This map will be
calculated against the GMM of the original complex map. The
EM restraint also has a “slope” variable which will persuade
movement of subunits to remain inside the map volume.
10. Finally, the mc1 variable will run the sampling of the subunit
bead models which have restraints added. Mc1 is an IMP
replica exchange macro which will additionally perform replica
exchange steps on flexible regions of the bead model. These
parameters will only affect flexible beads (see Note 14).
11. “crosslink_restraints” in mc1 adds the two xl1 and xl2
restraints to the replica exchange sampler.
12. A Bayesian scoring function is used to calculate the score of
each model per iteration (see Note 15). “number_of_best_scoring_models” controls how many output models are generated. These are saved within the “global_output_directory”
directory. The top scoring models are saved in the /output/
pdbs folder by default. Model names are updated and ranked
such that model.0.pdb has the highest score of the ensemble.
13. The per-iteration trajectory of the sampling simulation is saved
as /output/rmfs/0.rmf3. This file can be opened and played
using Chimera.
14. The PDB models generated by IMP only contain Ca atoms.
Since there are no missing residues (that have been modeled as
flexible beads), use PyMOL to align the alpha and beta subunits to model.0.pdb (see Note 16). You can then save this
atomistic model.
Table 2
Key parameters that can be used for the adjustment of modeling restraints
Heading
Function
Length
Distance threshold to enforce per iteration, set to 38 A ˚
Slope
Linear gradient for preventing the system from expanding too much
Columnmapping Designates the format of the stoichiometry.Txt file
Resolution
Sets the bead resolution that the cross-link distance will be measured using
Label
Label for modeling output
Csvfile
Toggle for stoichiometry.Txt file format to be read as a comma separated values file
234
Andy M. Lau and Argyris Politis
derived from the BS3 cross-linker molecule length (11 A ˚ ), two
lysine side chains (2 Â 7 A ˚ ) and an additional 10 A ˚ which
permits small-scale subunit translations and rotations and prevents the system from being locked into a particular
conformation.
9. The EM restraint is set by lines 171–178. In the first step, a
GMM map is calculated for each subunit. This map will be
calculated against the GMM of the original complex map. The
EM restraint also has a “slope” variable which will persuade
movement of subunits to remain inside the map volume.
10. Finally, the mc1 variable will run the sampling of the subunit
bead models which have restraints added. Mc1 is an IMP
replica exchange macro which will additionally perform replica
exchange steps on flexible regions of the bead model. These
parameters will only affect flexible beads (see Note 14).
11. “crosslink_restraints” in mc1 adds the two xl1 and xl2
restraints to the replica exchange sampler.
12. A Bayesian scoring function is used to calculate the score of
each model per iteration (see Note 15). “number_of_best_scoring_models” controls how many output models are generated. These are saved within the “global_output_directory”
directory. The top scoring models are saved in the /output/
pdbs folder by default. Model names are updated and ranked
such that model.0.pdb has the highest score of the ensemble.
13. The per-iteration trajectory of the sampling simulation is saved
as /output/rmfs/0.rmf3. This file can be opened and played
using Chimera.
14. The PDB models generated by IMP only contain Ca atoms.
Since there are no missing residues (that have been modeled as
flexible beads), use PyMOL to align the alpha and beta subunits to model.0.pdb (see Note 16). You can then save this
atomistic model.
Table 2
Key parameters that can be used for the adjustment of modeling restraints
Heading
Function
Length
Distance threshold to enforce per iteration, set to 38 A ˚
Slope
Linear gradient for preventing the system from expanding too much
Columnmapping Designates the format of the stoichiometry.Txt file
Resolution
Sets the bead resolution that the cross-link distance will be measured using
Label
Label for modeling output
Csvfile
Toggle for stoichiometry.Txt file format to be read as a comma separated values file
234
Andy M. Lau and Argyris Politis