Re: [ccp4bb] SSM superposition of a heterodimer of related chains such that A->B and B->A / SUMMARY

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

Previous message:
Subject: Re: SSM superposition of a heterodimer of related chains such that A->B and B->A / SUMMARY
From: Norbert Straeter strater {- at -} BBZ {- dot -} UNI-LEIPZIG {- dot -} DE
Date: 2010-02-17

Next message:
Subject: Post-Doctoral position at the University of Leicester, UK
From: Louise Fairall louise {- dot -} fairall {- at -} GOOGLEMAIL {- dot -} COM
Date: 2010-02-17

Subject: Re: SSM superposition of a heterodimer of related chains such that A->B and B->A / SUMMARY
From: Liz Potterton lizp {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-02-17

Norbert,

Sorry for this late reply. SSM will find multiple alternative matches
but most implementations just show you the 'best'. The Superposition
tool in CCP4mg uses ssm and has an option to look through the non-
optimal matches - hopefully one of these will be the one that you want.

Liz

On 17 Feb 2010, at 10:35, Norbert Straeter wrote:

> Dear All,
>
> last Friday I posted the following question:
>
> > I have a heterodimer of two related subunits (A and B). Now I
> > want to superimpose it using a secondary structure matching
> > (SSM) algorithm (e.g. CCP4 superpose or the coot algorithm)
> > such that the superposition matches A onto B and B onto A at
> > the same time. For a perfectly symmetrical closed C2 dimer,
> > it would not make a difference if I just superimposed A onto
> > B, but it is unsymmetrical. I know that this is easy to
> > specify in lsqkab when knowing the matching residue pairs.
> > Does anybody know an SSM program where I can specify the
> > chains to be superimposed (A->B and B->A)?
>
> Some replys described how to specify selections in pymol or coot for
> SSM alignment. To make it more clear, if you specify chains A+B as
> the moving selection and A+B or B+A as the reference, you will
> always get the best but trivial superposition of A->A and B->B. It
> appears as if there is currently no program for SSM superposition
> for which you can specify the chains to be matched if the structure
> that needs to be superimposed contains internal symmetry in form of
> different chains. As a workaround, one can rename chains and residue
> numbers before and after alignment:
>
>> OK, here's a possible inelegant solution, till something better comes
>> up....
>> Take dimer 1, and put it all into one chain X, keeping numbers for
>> A and
>> adding an offset eg 500 for the B chain. Take dimer 2, and put it
>> all into another chain Y, keeping the numbers
>> for B and adding the same offset to A.
>> Then do a match of chain X with chain Y.
>
> (Judith Murray-Rust)
>
>> Could it help to merge chains A and B first into two longer chains,
>> where
>> C=A+B
>> and
>> D=B+A ?
> (Matthias Zebisch)
>
> Using this strategy, you can probably use your favourite SSM
> alignment program. I just tested it within coot and it works.
>
>> Another strategy is the following:
>> One workaround would be to let SSM define the matching residues
>> (should
>> be the same for A->B and B->A) and input those in to lsqkab.
> (Herman Schreuder)
>
> Thanks to all, who provided help to this problem, also to Christian
> Roth, Gerard Kleywegt (use of "explicit" and "improve" commands in
> lsqman), Yu Wai Chen, Mark A. White, Christina Bourne, Markus
> Wiederstein (http://topmatch.services.came.sbg.ac.at/), Ed Pozharski
> and Regina Kettering.
>
> Norbert

CCP4bb navigation

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

Next message:
Subject: Post-Doctoral position at the University of Leicester, UK
From: Louise Fairall louise {- dot -} fairall {- at -} GOOGLEMAIL {- dot -} COM
Date: 2010-02-17