Re: [ccp4bb] RNA Torsion Angle Measurement Error

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: RNA Torsion Angle Measurement Error
From: Ben Akiyama akiyama {- at -} BIOLOGY {- dot -} UCSC {- dot -} EDU
Date: 2008-11-28

Next message:
Subject: Re: RNA Torsion Angle Measurement Error
From: Donnie Berkholz dberkholz {- at -} GENTOO {- dot -} ORG
Date: 2008-11-28

Subject: Re: RNA Torsion Angle Measurement Error
From: Ethan A Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-11-28

On Friday 28 November 2008, Ben Akiyama wrote:
> Hi Everyone,
>
> I am measuring and comparing torsion angles in several solved crystal
> structures of RNA helices using AMIGOS. I was wondering if anyone knows
> of a program that can give me an idea of the error in these measurements
> based on coordinate error, b-factors, etc.

If you mean real torsion angles, the only quantitative way to do this is
to do full-matrix refinement, invert the matrix, and derive error estimates
from the off-diagonal terms. That is not something you can do after the
fact from a previously refined structure.

On the other hand, perhaps you can provide more information about what
exactly is the question you want to answer.

For example, if you are interested in how reliable the assignment of sugar
puckers is, looking at torsion angles is not a good way to go about this.
I think you'd be better off counting satisfied/unsatisfied hydrogen bonding
partners for the ring oxygens.

Also, your mention of AMIGOS throws me off a bit. That program
calculates a pseudo-atom simplified representation of the model, right?
If you are asking about the pseudo-torsion angles associated with
pseudo-atoms, then I think there are no actual "measurements" directly
associated with them in the first place. Perhaps the paper describing
AMIGOS discusses the issue of how sensitive the simplified representation
is to small variation in the original coordinates? That's actually
an interesting question, but I don't have any intuitive feel for the answer.

--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: RNA Torsion Angle Measurement Error
From: Ben Akiyama akiyama {- at -} BIOLOGY {- dot -} UCSC {- dot -} EDU
Date: 2008-11-28

Next message:
Subject: Re: RNA Torsion Angle Measurement Error
From: Donnie Berkholz dberkholz {- at -} GENTOO {- dot -} ORG
Date: 2008-11-28