[buster-discuss] Watson-Crick bp restraints
Miguel Ortiz Lombardia
miguel.ortiz-lombardia at afmb.univ-mrs.fr
Thu Mar 18 09:58:12 CET 2010
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.
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.
> B. Martin Hallberg, PhD
> Junior research fellow
> Section for Cell Biology
> Department of Cell and Molecular Biology
> Karolinska Institutet
> 171 77 Stockholm
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