Subject: Re: [modeller_usage] Averaged RMSD for 100 models
From: Modeller Caretaker <>
Date: Thu, 01 Jun 2006 10:38:43 -0700
Cc:
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