Re: [ccp4bb] align DNA structures

- 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: structure validation tools
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-10-21

Next message:
Subject: Re: structure validation tools
From: Nathaniel Echols nathaniel {- dot -} echols {- at -} GMAIL {- dot -} COM
Date: 2009-10-21

Subject: Re: align DNA structures
From: Mark Brooks mark {- dot -} brooks {- at -} U-PSUD {- dot -} FR
Date: 2009-10-21

Anna Pyle's group came out with a powerful idea- a simplified set of
torsion angles for nucleic acids (NA).
http://nar.oxfordjournals.org/content/vol31/issue16/images/small/gkg682f1.gif
http://nar.oxfordjournals.org/cgi/content/abstract/31/16/4755

This is implemented in a Perl program, called PRIMOS (
http://www.pylelab.org/software/index.html ), which you use to
generate 'worms' corresponding to all the nucleic acid structures in
the database that you're working on. You then search with a worm
corresponding to the structure of interest.

It works very well for RNA, at least, but you have to download the
entire NDB yourself and make worms using the PERL scripts (store the
worms carefully, you don't want to do this more than once!).

A COOT or web (EBI?!) interface would be very welcome, since this
process is quite involved.

HTH,

Mark

2009/10/21 Mike England :
> Hi all,
>
> I will highly appreciate your help regarding following:
>
> How to align two DNA structures in Pymol or Coot or any other softwares?
> ( I tried regular "align" in Pymol, but it doesn't work for DNA; it
> works great for protein structures.)
>
>
> Thanks a lot in advance !
>
>
> Mike
>

--
Mark Brooks, IBBMC, UMR8619 - Bâtiment 430,
Université de Paris-Sud, 91405 Orsay, France.
Tel: (33) 169157968
Fax: (33) 169853715
Skype: markabrooks

CCP4bb navigation

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

Previous message:
Subject: Re: structure validation tools
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-10-21

Next message:
Subject: Re: structure validation tools
From: Nathaniel Echols nathaniel {- dot -} echols {- at -} GMAIL {- dot -} COM
Date: 2009-10-21