Re: [modeller_usage] Averaged RMSD for 100 models

Yun He wrote: > I have another question. How could I output the *Average* structure generated > in the MALIGN3D procedure? e.g, I have a NMR structure with 30 models, and I > want to get its average structure.

Use transfer_xyz after malign3d, with the cluster_cut option. This allows you to take the average of all structures, or the average of the largest cluster. See http://salilab.org/modeller/manual/node130.html

automodel will do this automatically for you, producing a 'cluster.ini' average structure and a 'cluster.opt', which is additionally optimized by conjugate gradients, if you call automodel.cluster() after automodel.make(). See http://salilab.org/modeller/manual/node54.html

Ben Webb, Modeller Caretaker