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--- On Tue, 6/21/11, biojava-l-request at lists.open-bio.org <biojava-l-request at lists.open-bio.org> wrote:

From: biojava-l-request at lists.open-bio.org <biojava-l-request at lists.open-bio.org>
Subject: Biojava-l Digest, Vol 101, Issue 8
To: biojava-l at lists.open-bio.org
Date: Tuesday, June 21, 2011, 1:00 PM

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Today's Topics:

   1. binning structures by quality.... (Jay Vyas)

----------------------------------------------------------------------

Message: 1
Date: Mon, 20 Jun 2011 12:31:32 -0400
From: Jay Vyas <jayunit100 at gmail.com>
Subject: [Biojava-l] binning structures by quality....
To: biojava-l at lists.open-bio.org
Message-ID: <BANLkTin3Fe-f5=iGF+G+TzHT9xwKsUgwXA at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Guys : I'm trying to bin some structures, about 30 of them.  I was
wondering if anyone knows the upper "limit" for a structure to have a
correct backbone, in RMSD units.  For example, a structure bundle with RMSD
of 9 would clearly have an undefined backbone, whereas a structure bundle
with an RMSD of 1 would definetely be precise enough to convey backbone
information.

I wanted a more precise bound.  I'm thinking, by eye, that anything above 4
angstroms is to imprecise to convey a backbone.

But I figured maybe there was a formal treatment of such RMSD "categories"
somewhere.

Any thoughts would be appreciated.

-- 
 Jay Vyas
MMSB/UCHC

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