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