Prepare MR Ensemble from Coordinate Data

MR Ensembles are superposed sets of sufficiently similar MR models, corresponding to the same target sequence. Using ensembles instead of singe models often increases chances of successful Molecular Replacement. This task uses MrBump software to make MR Ensemble from given structural homologs. The process is completely automatic and includes pruning structures according to the modification protocol and target sequence given, and bringing them in best superposition.

Pruning structures in MR Ensembles is done in order to remove parts that do not correspond to the target sequence; usually, this increases chances of successful Molecular Replacement. A few modification protocols are available in the task:

• Unmodified: atomic coordinates are not altered in any way

• Clip: water molecules and ligands are removed

• Molrep: modification protocol, based on the comparison of the target sequence and atomic coordinates, used by Molrep

• Sculptor: modification protocols, based on the comparison of the target sequence and atomic coordinates, provided by Phaser.Sculptor (cf. here)

• Chainsaw: modification protocols, based on the comparison of the target sequence and atomic coordinates, provided by Chainsaw

• Polyalanine: all residues are replaced with polyalanines

The resulting ensemble can be used in both Phaser and Molrep tasks, but the outcome may be different, especially in difficult cases.