[buster-discuss] DNA problem

[Nicolas Foos]

Dear Ed,

The problem come from the nomenclature DA/DT/DG/DC and 05'

You have to replace "  '  " by * and remove the DA by A. Your pdb is 
probably in V3.X pdb format. And i think your version of Buster is able 
to work with version 2.X of pdb format.

You may use emacs or something like that to correct manually your pdb file.

You can try to change the library use by your building program for pdb 
writting.

Example :

your pdb must to be with this form : For example : G

ATOM      1  P     G C   3     -12.196 -23.067   0.795  1.00
78.41           P
ATOM      2  O1P   G C   3     -12.512 -24.142  -0.144  1.00
74.58           O
ATOM      3  O2P   G C   3     -10.891 -22.925   1.347  1.00
76.76           O
ATOM      4  O5*   G C   3     -13.052 -23.374   2.047  1.00
72.14           O
ATOM      5  C5*   G C   3     -14.419 -23.366   1.863  1.00
61.60           C
ATOM      6  C4*   G C   3     -15.148 -23.656   3.141  1.00
56.54           C
ATOM      7  O4*   G C   3     -15.094 -25.090   3.167  1.00
50.50           O
ATOM      8  C3*   G C   3     -14.514 -23.094   4.424  1.00
45.25           C
ATOM      9  O3*   G C   3     -15.402 -22.397   5.317  1.00
38.52           O
ATOM     10  C2*   G C   3     -13.962 -24.334   5.103  1.00
44.88           C
ATOM     11  C1*   G C   3     -14.745 -25.462   4.458  1.00
37.32           C
ATOM     12  N9    G C   3     -13.979 -26.649   4.313  1.00
20.00           N
ATOM     13  C8    G C   3     -12.938 -26.842   3.483  1.00
20.00           C
ATOM     14  N7    G C   3     -12.453 -28.012   3.567  1.00
20.00           N
ATOM     15  C5    G C   3     -13.232 -28.612   4.500  1.00
20.00           C
ATOM     16  C4    G C   3     -14.196 -27.786   4.984  1.00
20.00           C
ATOM     17  N1    G C   3     -14.112 -30.088   5.930  1.00
20.00           N
ATOM     18  C2    G C   3     -15.046 -29.194   6.343  1.00
20.00           C
ATOM     19  N3    G C   3     -15.156 -27.975   5.903  1.00
20.00           N
ATOM     20  C6    G C   3     -13.143 -29.900   4.991  1.00
20.00           C
ATOM     21  O6    G C   3     -12.358 -30.795   4.724  1.00
20.00           O
ATOM     22  N2    G C   3     -15.861 -29.709   7.276  1.00
20.00           N


  I Hope my contribution to your problem is not out of date and help you.

Nicolas

Le 20/05/13 16:30, Ed Pozharski a écrit :
> I am trying to refine a model that contains DNA.  PDB file is, I
> believe, in v3 nomenclature (DA/DT/DG/DC and O5' etc).  Refinement fails
> early and I get the warning that the pdb file
>
> "contains a majority of nucleic acids with ribose names O5' not O5*"
>
> It suggests I run pdbvconv, which I do but that says
>
> "v3 DNA names not detected"
>
> and leaves the pdb file unchanged.  I didn't try renaming everything
> back to v2 manually yet and did not really dig deep into the problem.
> My hope is that I am missing something trivial that can be quickly
> resolved.
>
> I am running v.2.1.0.
>
> Cheers,
>
> Ed.
>


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