Re: [modeller_usage] Averaged RMSD for 100 models

[Yun He <>]

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