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.
On Thursday 01 June 2006 00:46, Modeller Caretaker wrote: > Robert Selwyne wrote: > > I had run MODELLER to produced model 1-100.pdb (100 models) of same acid > > sequence but different energy values. Now, i want to calculate the RMSD > > values for the models. I know that SUPERPOSE will do for me. But i > > couldnot correlate and implement the results. > > You can align multiple structures with alignment.compare_structures() > (see http://salilab.org/modeller/manual/node193.html), > alignment.malign3d() (see > http://salilab.org/modeller/manual/node195.html) or alignment.salign(). > > > Say in VMD 1.8.4 in the RMSD calculator option, if *Average* is > > selected, VMD first computes the average x, y, z coordinates of the > > selected atoms in each molecule, then computes the RMS distance of each > > molecule from that average structure. > > This is essentially the same algorithm used by alignment.malign3d(). See > the manual linked above. > > There is an example in examples/commands/malign3d.py. If you are using > automodel to build your models, you can ask it to automatically align > the generated models and calculate many properties, including the RMS, > by setting final_malign3d to True. See examples/automodel/model-fast.py > for an example. > > Ben Webb, Modeller Caretaker