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Author Topic: the center of a dimer step  (Read 11319 times)

Offline feix

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the center of a dimer step
« on: September 29, 2006, 01:53:02 pm »
HI! Xiangjun:
In which file among the 3DNA output files can I find the center of a dimer step?
Thanks a lot!
Fei

Offline xiangjun

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« Reply #1 on: September 29, 2006, 10:45:13 pm »
Hi Fei,

If I understand you correctly, you are looking for the middle-reference-frame, which is available from file auxiliary.par after  running analyze on a duplex struture. An example would be as follows:
Code: [Select]
find_pair bdl084.pdb stdout | analyzeCheck file auxiliary.par, the section you are looking for is:
Code: [Select]
*****************************************************************************************
Local middle reference frames
                Ox      Oy      Oz     Xx    Xy    Xz   Yx    Yy    Yz    Zx    Zy    Zz
   1 CG/CG    16.84   25.38   24.41 -0.90  0.43 -0.02  0.40  0.82 -0.41 -0.16 -0.38 -0.91
   2 GC/GC    16.36   24.39   21.11 -0.46  0.84 -0.28  0.86  0.36 -0.36 -0.20 -0.40 -0.89
   3 CG/CG    16.17   23.28   17.92  0.11  0.90 -0.41  0.98 -0.17 -0.12 -0.18 -0.39 -0.90
   4 GA/TC    15.72   21.96   15.03  0.62  0.71 -0.33  0.77 -0.63  0.07 -0.16 -0.30 -0.94
   5 AA/TT    15.07   21.01   11.89  0.96  0.19 -0.20  0.24 -0.94  0.26 -0.14 -0.30 -0.94
   6 AT/AT    14.73   20.48    8.65  0.92 -0.39 -0.03 -0.36 -0.87  0.33 -0.16 -0.29 -0.94
   7 TT/AA    14.44   19.97    5.45  0.57 -0.81  0.13 -0.80 -0.52  0.30 -0.17 -0.27 -0.95
   8 TC/GA    14.15   19.36    2.16 -0.05 -0.97  0.25 -0.99  0.09  0.14 -0.16 -0.24 -0.96
   9 CG/CG    13.18   18.67   -0.90 -0.59 -0.74  0.31 -0.78  0.62  0.01 -0.20 -0.24 -0.95
  10 GC/GC    12.62   18.30   -4.04 -0.93 -0.27  0.23 -0.31  0.94 -0.14 -0.18 -0.20 -0.96
  11 CG/CG    12.80   18.15   -7.43 -0.93  0.35  0.11  0.33  0.93 -0.18 -0.16 -0.13 -0.98
*****************************************************************************************

HTH,

Xiangjun

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.