[phenixbb] hydrogen-bond restraints for Watson-Crick base pairs

Nathaniel Echols nechols at lbl.gov
Tue Jun 22 15:03:45 PDT 2010

On Tue, Jun 22, 2010 at 2:56 PM, Scott Classen <sclassen at lbl.gov> wrote:

> I set main.secondary_structure_restraints = True
> and it appears that protein ss elements are found and added to the geo
> file, but watson crick pairs are not.
> My DNA looks like this:
> HETATM    1  O5*  Ad D   1     -47.740 -49.121 -17.972  1.00 91.44
>   O
> ANISOU    1  O5*  Ad D   1    13002   6701  15042   3404   -258  -1747
>   O
> Is there any reason it wouldn't be recognized by PROBE?

Jeff says that PROBE probably won't recognize "Ad" (it expects "dA"
instead), and the default behavior probably requires O5', not O5*.  The atom
naming we can probably work around, the residue names are more difficult.
 What program generated these residues?

If you can send us the model (or just enough of it to have base pairs,
actually), we'll take a look.

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