How to read the out put file of 3DNA

[malsha]

Hi,
Does anyone know how to read the information of RMSD of the bases of out file?? I'm sorry I'm new to 3DNA  and I have no clue what it says.
This is the out put file that i got.

RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

            Strand I                    Strand II          Helix
   1   (0.046) ...1>-:...2_:[.DA]A-----T[.DT]:..11_:-<...1 (0.038)     |
   2   (0.051) ...1>-:...3_:[.DT]T-----A[.DA]:..10_:-<...1 (0.076)     |
   3   (0.036) ...1>-:...4_:[.DT]T-----A[.DA]:...9_:-<...1 (0.041)     |
   4   (0.052) ...1>-:...5_:[.DG]G-----C[.DC]:...8_:-<...1 (0.041)     |
   5   (0.057) ...1>-:...6_:[.DG]G-----C[.DC]:...7_:-<...1 (0.032)     |
   6   (0.038) ...1>-:...7_:[.DC]C-----G[.DG]:...6_:-<...1 (0.095)     |
   7   (0.056) ...1>-:...8_:[.DC]C-----G[.DG]:...5_:-<...1 (0.045)     |
   8   (0.097) ...1>-:...9_:[.DA]A-----T[.DT]:...4_:-<...1 (0.050)     |
   9   (0.066) ...1>-:..10_:[.DT]T-----A[.DA]:...3_:-<...1 (0.068)     |
  10   (0.055) ...1>-:..11_:[.DG]G-----C[.DC]:...2_:-<...1 (0.043)     |
  11   (0.032) ...1>-:..12_:[.DC]C-----G[.DG]:...1_:-<...1 (0.051)     |

Thank you in advance!!

[xiangjun]

Hi,

The RMSD is the root-mean-square deviation between ring atoms of each base in the analyzed structure and the corresponding standard reference frames. It is normally quite small (< 0.1 Å), due to the rigid planarity of base rings. Please see the first two sections of "tech-details.pdf" in the $X3DNA/doc directory of the 3DNA distribution for more information.

This is the out put file that i got.

RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

            Strand I                    Strand II          Helix
   1   (0.046) ...1>-:...2_:[.DA]A-----T[.DT]:..11_:-<...1 (0.038)     |

From the question, I assume that you have been able to successfully get 3DNA up and running. For the benefit of other new 3DNA users, could you please post a follow-up to the thread "How to 3DNA set environment variables on Linux?"? Thanks!

Best regards,

Xiang-Jun

[malsha]

Thank you Sir!
What I exactly want to know is what does it mean by this?
1>-:...2_:[.DA]A-----T[.DT]:..11_:-<...1
Is DA and DT denote the base plane of Adenine and Thymine respectively and can you please explain me what are those numbers??

[xiangjun]

1>-:...2_:[.DA]A-----T[.DT]:..11_:-<...1

This is an ad hoc format specifying the two nucleotides in a pair. Starting from the left, 1>-:...2_:[.DA]A, here 1 means model number, 2 is the residue sequence number, and DA is the residue name, and A is the one-letter abbreviation. So here it means A (named DA for DNA) with sequence number of 2, in model number 1. The same idea applies to the right hand side, just with order reversed. Please see http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html for a description of the Coordinate Section of the PDB format.

I know this cryptic format is not intuitive, and not well documented. However, it has been there for so long, and it will stay with the 3DNA v2.x releases. If you have tried DSSR, the residue identifier is much more flexible, and well documented (the --idstr option, see the "DSSR User Manual").

HTH,

Xiang-Jun

[malsha]

Okay thank you very much Sir!