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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
--
modeller-care@salilab.org             http://www.salilab.org/modeller/
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