Re: [modeller_usage] native overlap of pdb structures

On 03/06/2015 10:55 PM, Mouses Stamboulian wrote: > I'm not getting such good overlaps within 5 angstroms. my question is > that is there a way to refine my final comparative Model so that I'll > get better (higher) native overlap values? Thank you.

I'm not sure what you're asking here is why Modeller is reporting a different RMSD to whatever other method you're using, or how do you improve the RMSD? In the first case, note that superpose performs a superposition without changing the alignment - that won't always give you the "best" RMSD. (SALIGN can also do a structural alignment.) In the second case, that's kind of a broad question.

Ben Webb, Modeller Caretaker