Re: [modeller_usage] Averaged RMSD for 100 models

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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