1cdp 1.60 0.16 0.702 62. Conclusions Most modelling procedures use the backbone of the template as the backbone of the model, and add the sidechains onto this backbone. The RMSe of the backbone will therefore be the same as the RMSd of the model and template backbone. We call this the starting error. Obviously under normal conditions the final all atom RMSe will always be bigger than this starting error.
Loops normally have roughly a similar conformation in similar structures.
A weak correlation is found between differences in loop conformations and mutations involving proline or glycine. However, if loops are not predicted well, this is most often the result of differences in symmetry contacts between these loops in the model and the template structure. There is a basic error of up to 0.5 A in the backbone of every model, just as a result of uncertainties in the experimental structures. Of course many models will have lower backbone RMS than 1.0 A. The problem, however is that in practical cases one does not know how good the models are. Groningen, The Netherlands.