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Author Topic: local helical axis  (Read 6158 times)

Offline feixu

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local helical axis
« on: April 19, 2012, 12:23:34 pm »
HI!
I am building a uniform helix with repeating values of step parameters. In this way, the local helical axis is the same for every step. I want to put the local helical axis in  at the center and perpendicular to the bottom of my figure. Where can I find the vectors of the local helical axis? Are they contained in the ref_frames.dat generated by the 'rebuild' command?

Thanks a lot!

Fei

Offline xiangjun

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Re: local helical axis
« Reply #1 on: April 19, 2012, 03:31:20 pm »
Does the section (from analyze output) as below fit the bill? Here I am using 355d/bdl084 as an example.

Code: [Select]
Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
         for each dinucleotide step

     step       Px        Py        Pz        Hx        Hy        Hz
   1 CG/CG     15.99     26.43     24.17      0.03     -0.21     -0.98
   2 GC/GC     17.37     23.05     21.31     -0.39     -0.41     -0.82
   3 CG/CG     15.84     24.53     17.27      0.23     -0.39     -0.89
   4 GA/TC     15.59     22.51     14.84     -0.16     -0.35     -0.92
   5 AA/TT     15.65     20.84     11.86     -0.14     -0.31     -0.94
   6 AT/AT     15.26     20.22      8.64     -0.14     -0.22     -0.97
   7 TT/AA     15.05     19.77      5.44     -0.12     -0.30     -0.95
   8 TC/GA     14.55     19.21      2.15     -0.12     -0.26     -0.96
   9 CG/CG     11.86     20.64     -0.66     -0.23     -0.04     -0.97
  10 GC/GC     14.37     17.46     -3.79     -0.05     -0.38     -0.93
  11 CG/CG     12.05     18.00     -7.38     -0.08      0.04     -1.00

Xiang-Jun
« Last Edit: April 19, 2012, 04:08:31 pm by xiangjun »

Offline feixu

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Re: local helical axis
« Reply #2 on: April 19, 2012, 04:44:42 pm »
Hi! Xiangjun:
I created a file containing the values of step parameters like this:

8 # base-pairs
   0 # ***local base-pair & step parameters***
  #   Shear Stretch Stagger  Buckle Prop-Tw Opening   Shift   Slide    Rise    Tilt    Roll   Twist
A-T     0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
A-T     0.00    0.00    0.00    0.00    0.00    0.00   -2.67    0.52    3.25  -13.51    6.10 -101.59
A-T     0.00    0.00    0.00    0.00    0.00    0.00   -2.67    0.52    3.25  -13.51    6.10 -101.59
A-T     0.00    0.00    0.00    0.00    0.00    0.00   -2.67    0.52    3.25  -13.51    6.10 -101.59
........
Then I used 'rebuild' command. The output file was ref_frames.dat and an .alc file. The ref_frames.dat is as below:

8 base-pairs
...     1 A-T ...
    0.0000    0.0000    0.0000
    1.0000    0.0000    0.0000
    0.0000    1.0000    0.0000
    0.0000    0.0000    1.0000
...     2 A-T ...
   -0.8746    2.5068    3.3034
   -0.1866   -0.9758    0.1141
    0.9508   -0.2086   -0.2290
    0.2472    0.0658    0.9667
...     3 A-T ...
    2.4889    3.0548    5.8231
   -0.8648    0.3931    0.3125
   -0.4323   -0.8994   -0.0651
    0.2554   -0.1914    0.9477
(....base pair 4-5)
...     7 A-T ...
    5.0245    0.8174   17.2665
   -0.2431    0.9359    0.2549
   -0.9621   -0.2662    0.0597
    0.1237   -0.2307    0.9651
...     8 A-T ...
    3.2341   -1.4303   20.3816
    0.9983    0.0588    0.0043
   -0.0588    0.9982    0.0089
   -0.0038   -0.0091    1.0000
~                             

I guess, the first line for each base pair is a origin and the other three lines are a middle frame. I used the repeating values of step parameters so the vector of local helical axis of each step should be the same. I wonder where is the vectors of the local helical axis. I also attach a sample figure I made. I need to know the local helical axis and rotate it to a perpendicular position.

Best,

Fei

Offline xiangjun

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Re: local helical axis
« Reply #3 on: April 20, 2012, 09:44:21 am »
In my previous reply, I asked you if the "Position (Px, Py, Pz) and local helical axis vector" from analyze output file are what you want. From my understanding of your question "Where can I find the vectors of the local helical axis?", I guess they should be. Please confirm.

The "ref_frames.dat" file, as its name implies, contains the reference frames of all base pairs.

Xiang-Jun

Offline feixu

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Re: local helical axis
« Reply #4 on: April 20, 2012, 11:06:07 am »
I understand now. I think, I can do in two ways: (1) I can rebuild an atomic structure, then analyze the structure to obtain the local helical axis,  (2) I can use matlab to compute a local helical axis with the algorithm introduced in the manual.

Thanks,

Fei

 

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.