Sentence examples for manually rebuilt and from inspiring English sources

After placing the ligand into the electron density map, the model of the complex was manually rebuilt and refined through iterative cycles in Coot and Phenix.

The model was refined using AutoBuster and manually rebuilt in COOT 0.6.2 and O 10.0.3.

Models were then mutated to the correct amino acid and manually rebuilt in Coot (Emsley and Cowtan, 2004).

The initial model was then manually rebuilt in COOT and refined with PHENIX.

Individual domain of previous KATP models (PDB: 5WUA and 5TWV) and CFTR in Mg-ATP bound state (PDB: 5W81) were used as the initial model, docked into cryo-EM map with best local quality of that region by chimera and manually rebuilt in Coot according to the density (Emsley et al., 2010).

The structure was refined in BUSTER (v. 2.10.1) at 3.8 Å using TLS refinement strategy (Bricogne et al., 2011) and manually rebuilt in Coot (Emsley et al., 2010).

The initial model was traced automatically using the program BUCCANEER and was manually rebuilt in COOT.

The model was refined with refmac [39], using TLS and applying non-crystallographic symmetry restraints, and models were manually rebuilt with Coot [40].

Several regions (residues 27 40, 53 60, 89 97, and 297 309) that display substantial difference between the model and electron density were manually rebuilt using the program O [38] according to difference density maps and simulated annealing omit maps.

The structure was manually rebuilt using the O program [35] and refined with the CNS program, with or without twin refinement.

The resulting crude model was manually rebuilt to remove clashes where possible and finally energy-minimised using GROMACS (Lindahl et al, 2001) with a simulated annealing protocol.