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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
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Does the section (from analyze output) as below fit the bill? Here I am using 355d/bdl084 as an example.
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
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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
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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
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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
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