[buster-discuss] buster and DNA?

[Nicolas Foos]

Le 11/06/10 17:16, Sabine Schneider a écrit :
> Hello,
>
> I am want to refine a protein-DNA complex in buster, but I am struggling
> with the nomenclature for DNA.
> If I add DNA to the pdb file, buster fails with the following error
> message despite that there is a dictionary for the nucleotides:
>
> WARNING : using geometric restraints for Gd from file
>             /home/sabine/Progs/buster-2.8/tnt/data/ccp4/Gd.dic:
>             this file was generated automatically using the
>             CCP4/Refmac distributed dictionaries. Although we
>             believe them to be of good quality, it was not
>             checked manually. Therefore, it is supplied
>             without any guarantee - if you prefer your own
>             geometric restraints dictionary, please create it
>             with one of the programs in the MakeTNT toolbox
>             and supply it directly (see documentation).
>
>
> I also tried changing it to GD, GUA, G as well as swapping the * for ',
> O1P to OP1 and so on....
> In addition I generated a dictionary file using TNT which also failed.
>
> Any help is much appreciated!
>
> Sabine
>
>
>
>    
Hello Sabine,

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

The important, is to remove the "d" after G or A T C wich come in the 
Coot output for example.

And if necessary writte O with * like in the example.

I hope to give you some help.

Nicolas.


-- 
Nicolas Foos, PhD Student
Molecular Transport&  Signalling
AFMB UMR 6098 CNRS/UI/UII Case 932
163 Avenue de Luminy
13288 Marseille cedex 9 (France)
Tel : +33 4 91 82 55 60
Fax : +33 4 91 26 67 20
e-mail : Nicolas.Foos at afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/


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