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Re: [ccp4bb] practical limits of MR?
 

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CCP4bb <-- 2007 <-- March 2007 <-- 05 March 2007
Previous message:
Subject: practical limits of MR?
From: Nat Echols echols {- at -} UCLINK {- dot -} BERKELEY {- dot -} EDU
Date: 2007-03-05 		Next message:
Subject: Re: practical limits of MR?
From: Bart Hazes bart {- dot -} hazes {- at -} UALBERTA {- dot -} CA
Date: 2007-03-05


Subject: Re: practical limits of MR?
From: "Santarsiero, Bernard D {- dot -} " bds {- at -} UIC {- dot -} EDU
Date: 2007-03-05
On Mon, March 5, 2007 2:16 pm, Nat Echols wrote:
> I had a debate with a coworker about using MR in desperation and I'm
> curious what the most extreme case is where a very different model was
> used to solve a structure. This could be highest RMSD, lowest % identity,
> or most incomplete model. I'm also curious whether homology modelling has
> ever been useful for this. (I'm pretty sure I've come across papers
> discussing this last concept.)
>
> thanks,
> Nat
>

I'm not sure what "in desperation" means. You're trying to solve a
structure, so all options are open, right? They don't have to be elegant,
it just has to work. :)

I know of a few cases where roughly 15% of a structure was used as a
search model to solve a structure. Recently I used about 30% of the
structure to get the initial model with MR, and then bootstrap along to
find the remainder. Similarly, you can get away with 25-30% sequence
homology (so long as there is high structural homology) with MR. It's
relatively easy to find a helix-turn-helix motif by MR than, say, an
extended beta-sheet expanse, because the beta-sheet can substantially bend
and twist, whereas the helices are fairly rigid.

Bernie Santarsiero

CCP4bb navigation

CCP4bb <-- 2007 <-- March 2007 <-- 05 March 2007
Previous message:
Subject: practical limits of MR?
From: Nat Echols echols {- at -} UCLINK {- dot -} BERKELEY {- dot -} EDU
Date: 2007-03-05 		Next message:
Subject: Re: practical limits of MR?
From: Bart Hazes bart {- dot -} hazes {- at -} UALBERTA {- dot -} CA
Date: 2007-03-05


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