Instead of using a very generic model containing a lot of variability, we suggest to use an initial model, which contains only a variability in identity, and then use a specific model, containing variability in pose and expression.
The structures were solved by molecular replacement with the PHENIX software suite using an initial search model composed of the Tth 70S ribosome (PDB ID codes 2WDG, 2WDH, 2WDI, and 2WDJ) with all ligands and ions removed.
TyrBm structure with KA at the entrance to the active site was used as an initial model to run an extensive non-biased ligand migration simulations with PELE Protein Energy Landscape Explorationn) in a constrained sphere of 20 Å (from the initial ligand center of mass 38.
When relocating events, the P-wave velocity model is used as an initial model.
The velocity model of Akyol et al. (2006) was used as an initial model.
The reconstruction after refinement was used as an initial model for the further single particle data processing.
This model was then used as an initial model and also as a new prior model for another series of iterative inversions.
The model obtained by the tau-p method and tomography analysis was used as an initial model for the ray tracing method.
Therefore, this can be considered an approximation of the stress drop that can be used as an initial model for dynamic rupture simulation.
