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Questions and answers => General discussions (Q&As) => Topic started by: PRZEMEK on August 24, 2006, 02:48:33 am

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Title: problems with find pair dont recognize modificated base pair
Post by: PRZEMEK on August 24, 2006, 02:48:33 am

Hi
>
> Im work with X3DNA, im try use this program to analyze structure of
> modificated dna strands. I hawe create nucleic acid strand witch is
> build from 24 base pairs one of them was modificated and molecule off
> guanine was replaced by 8oxoguanine this structure was writen on the end
> of pdb file as molecule number 49. I hawe problem with creating input
> file because program dont recognize base pair wich contain 8oxoguanine
> molecule. I had modificated basepair.dat file and add ATOMIC.PDB file of
> 8oxoguanie. what schould i do to corectly describe this structure.
>                     Przemek Czeleñ

Title:
Post by: xiangjun on August 24, 2006, 09:01:05 pm

The problem you have is because of the non-standard atomic names of the modified 8oxoguanine.  This will become immediately obvious if you display this residue using Rasmol and "label %a". For example, you do not have the " N9 " atom, instead you have " N4 " connecting to " C6 ". 3DNA uses the standard atomic names to identify a residue.

Code: [Select]

ATOM      1  O1  8og     1       3.537   1.423  -0.000  1.00  0.00
ATOM      2  C4  8og     1       3.852   0.232  -0.000  1.00  0.00
ATOM      3  N1  8og     1       2.854  -0.789  -0.000  1.00  0.00
ATOM      4  C1  8og     1       3.077  -2.143  -0.000  1.00  0.00
ATOM      5  N5  8og     1       1.984  -2.956  -0.000  1.00  0.00
ATOM      6  N2  8og     1       4.278  -2.684  -0.000  1.00  0.00
ATOM      7  C2  8og     1       5.269  -1.754  -0.000  1.00  0.00
ATOM      8  C3  8og     1       5.134  -0.380  -0.000  1.00  0.00
ATOM      9  N3  8og     1       6.409   0.160  -0.000  1.00  0.00
ATOM     10  C5  8og     1       7.365  -0.843  -0.000  1.00  0.00
ATOM     11  O2  8og     1       8.589  -0.742  -0.000  1.00  0.00
ATOM     12  N4  8og     1       6.615  -2.035  -0.000  1.00  0.00
ATOM     13  C6  8og     1       7.224  -3.350  -0.000  1.00  0.00In addition, there is already an entry for 8OG in file baselist.dat

Code: [Select]

8OG     g      #       pdb1fyi
so you need not to add an extra line for it. Indeed it helps to download pdb1fyi to see how atoms are named for 8OG over there.

When adding a new base into baselist.dat, please use all uppercase letters: thus use "8OG" instead of "8og".

HTH,

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University