Re: [modeller_usage] native overlap of pdb structures
To: Mouses Stamboulian <>, "" <>
Subject: Re: [modeller_usage] native overlap of pdb structures
From: Modeller Caretaker <>
Date: Tue, 10 Mar 2015 17:13:10 -0700
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.