[buster-discuss] Watson-Crick bp restraints

[Miguel Ortiz Lombardia]

Hi Martin,

Including the following lines in a file passed to Gelly:

NOTE BUSTER_DISTANCE =2.95 0.05 A|1:O4 B|2:N6
NOTE BUSTER_DISTANCE =2.82 0.05 A|1:N3 B|2:N1
NOTE BUSTER_DISTANCE =3.63 0.05 A|1:O4 B|2:N1
NOTE BUSTER_DISTANCE =5.40 0.05 A|1:O2 B|2:N6

NOTE BUSTER_DISTANCE =2.91 0.05 A|2:N4 B|1:O6
NOTE BUSTER_DISTANCE =2.95 0.05 A|2:N3 B|1:N1
NOTE BUSTER_DISTANCE =2.86 0.05 A|2:O2 B|1:N2
NOTE BUSTER_DISTANCE =3.65 0.05 A|2:N3 B|1:N2
NOTE BUSTER_DISTANCE =5.42 0.05 A|2:O2 B|1:O6

should work, assuming your DNA simply contains the dinucleotide d(TC:AG). You should extend it similarly for a longer sequence.

It is based on the old brestraints.inp from XPLOR and I haven't used it myself so far. Quite probably you will need to play with the sigma values. Possibly other people has advice to give regarding sigmas.

Good luck!


Miguel

Le 16 mars 2010 à 08:50, Martin Hallberg a écrit :

> Dear All,
> What is the best way to restrain Watson-Crick base pairs in the Buster package?
> I am suffering at ~4 Å with an RNA structure and I gather it would be really good have them.
> 
> Cheers,
> 
> Martin
> 
> .
> B. Martin Hallberg, PhD
> Junior research fellow
> Section for Cell Biology
> Department of Cell and Molecular Biology
> Karolinska Institutet
> 171 77 Stockholm
> Sweden
> http://tinyurl.com/yzn9y5j
> 
> 
> 
> 
> 
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-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
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e-mail: miguel.ortiz-lombardia at afmb.univ-mrs.fr
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