Re: [ccp4bb] Tough Low-Res MR

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CCP4bb <-- 2008 <-- February 2008 <-- 21 February 2008

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From: "Santarsiero, Bernard D {- dot -} " bds {- at -} UIC {- dot -} EDU
Date: 2008-02-21

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Date: 2008-02-21

Subject: Re: Tough Low-Res MR
From: Jan Abendroth jan {- dot -} abendroth {- at -} GMAIL {- dot -} COM
Date: 2008-02-21

Hi all,
just to second previous statements: Phaser has done wonders for me in a few
tough cases, also at low resolution: Eg. various 6-10AA data sets with
highly homologous search models. Or a rather bad search model: 1.8AA rmsd
over ~50% of the residues. Often up to a point where the solution was
correct, however model bias did not allow to get further.
Sometimes it turned out to be helpful to increase the numbers of rotation
solutions that are considered for the translation search.

Cheers
Jan

##
deCODE biostructures
Bainbridge Island

2008/2/21, Roger Rowlett :
>
> James Stroud wrote:
> > Hello All,
> >
> > I have a tough ~3.5 Å (pushing it) MR problem where I have a solution
> > of sorts, but because I'm working with a heterodimer of two closely
> > related subunits (with two such heterodimers in the ASU) I have a 2**2
> > possibilities for the arrangement of these subunits in the ASU. Each
> > subunit is composed of two more-or-less independent domains. Basically
> > I'm looking for the best possible software to disambiguate this
> > problem. I usually use CNS for these problems, but I think I may have
> > exhausted its capabilities. I've heard that there have been some
> > advances in MR in recent years, but I haven't kept up with all of the
> > software. Does anyone have suggestions for packages to try?
> >
> > James
> >
> > --
> > James Stroud
> > UCLA-DOE Institute for Genomics and Proteomics
> > Box 951570
> > Los Angeles, CA 90095
> >
> > http://www.jamesstroud.com
> >
>
> Phaser and EPMR (now Open-EPMR) are among the best, and EPMR may
> actually work better in some cases without high resolution data. We've
> solved some really tough nuts to crack with both of these, and they are
> pretty fast to boot.
>
> Cheers,
>
>
> --
> ------------------------------------------------------------------------
> Roger S. Rowlett
> Professor
> Colgate University Presidential Scholar
> Department of Chemistry
> Colgate University
> 13 Oak Drive
> Hamilton, NY 13346
>
> tel: (315)-228-7245
> ofc: (315)-228-7395
> fax: (315)-228-7935
> email: rrowlett@mail.colgate.edu
>

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CCP4bb <-- 2008 <-- February 2008 <-- 21 February 2008

Previous message:
Subject: Re: XDS and overlaps
From: "Santarsiero, Bernard D {- dot -} " bds {- at -} UIC {- dot -} EDU
Date: 2008-02-21

Next message:
Subject: Re: XDS and overlaps
From: proclus {- at -} GNU-DARWIN {- dot -} ORG proclus {- at -} GNU-DARWIN {- dot -} ORG
Date: 2008-02-21