[buster-discuss] buster and DNA?
Nicolas Foos
Nicolas.Foos at afmb.univ-mrs.fr
Sat Jun 12 13:53:18 CEST 2010
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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