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Hi G, >Dear all, > >I have several similar models which can be superimposed. (looks like NMR >solved structure) Then I made those superimposed models to be a single >ensemble in phaser. > >My question is: > >what would be the difference of running phaser with this kind of ensemble >and with an ensemble which include only one model? As I have B factor >information in PDB, the uncertainty in model has already been considered >even if I just provide one model. Is that right? Would that really be more >helpful to test an ensemble with multiple models superimposed? Although I am not aware of any systematic study, there are indications that an ensemble can be a better model than a single model with B-factor weighting (check out the phaser MR tutorial with toxd). For one thing, an ensemble will weight up the structurally conserved parts of the model, while this is not guaranteed with B-factors (although both tends to weight up the core and weight down the surface). Also, B-factors are normally restricted to describe an isotropic uncertainty, but ensembles can describe complex motions of loops, etc. > > What would happen if those superimposed models are not quite similar, or > they can not superimposed well( some distance between them can be > observed)? It is possibly a good idea to do a weighted superposition, so that only the structurally similar parts are superposed (this is automatically done by the SSM algorithm). If there are still major deviations, you can consider "trimming" these residues away. This is something that can be done automatically with "ensembler" (currently in PHENIX, but eventually to be included in CCP4 as well). BW, Gabor > >Many thanks, >G >