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Questions and answers => General discussions (Q&As) => Topic started by: thenmalar on May 17, 2012, 12:08:10 pm

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Title: 3DNA with twist and rise calculated w.r.t c1'
Post by: thenmalar on May 17, 2012, 12:08:10 pm

 Hi Xiang,

   I am wondering whether it is possible to get a 3DNA version which has the twist and rise calculated with respect to C1' atoms of the base pair.

Thanks in advance,
Thenmalar
Title: Re: 3DNA with twist and rise calculated w.r.t c1'
Post by: xiangjun on May 17, 2012, 12:30:41 pm
Try 'cehs' instead of 'analyze'. Does it provide what you want?

Xiang-Jun
Title: Re: 3DNA with twist and rise calculated w.r.t c1'
Post by: thenmalar on May 18, 2012, 06:42:35 am
Hi,

  I am looking for something like the following that was available in the earlier version of 3DNA:


Global parameters based on C1'-C1' vectors:

disp.: displacement of the middle C1'-C1' point from the helix
angle: inclination between C1'-C1' vector and helix (subtracted from 90)
twist: helical twist angle between consecutive C1'-C1' vectors
rise:  helical rise by projection of the vector connecting consecutive
       C1'-C1' middle points onto the helical axis

     bp       disp.    angle     twist      rise
   1 C-G      5.09     -8.41     41.13      3.65


Thanks,
Thenmalar
Title: Re: 3DNA with twist and rise calculated w.r.t c1'
Post by: xiangjun on May 18, 2012, 07:12:26 am
Thanks for clarifying your question. The info you asked for is still available in 3DNA output from 'analyze' as shown below for 355d/bdl084:
****************************************************************************
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 3.30(0.52)
Helix:    -0.127  -0.275  -0.953
HETATM 9998  XS    X X 999      17.536  25.713  25.665
HETATM 9999  XE    X X 999      12.911  15.677  -9.080
Average and standard deviation of helix radius:
      P: 9.42(0.82), O4': 6.37(0.85),  C1': 5.85(0.86)

Global parameters based on C1'-C1' vectors:

disp.: displacement of the middle C1'-C1' point from the helix
angle: inclination between C1'-C1' vector and helix (subtracted from 90)
twist: helical twist angle between consecutive C1'-C1' vectors
rise:  helical rise by projection of the vector connecting consecutive
       C1'-C1' middle points onto the helical axis

     bp       disp.    angle     twist      rise
   1 C-G      1.95      5.18     36.25      3.50
   2 G-C      2.04      4.65     40.52      2.43
   3 C-G      2.26      4.02     28.36      4.27
   4 G-C      3.04     -0.22     36.02      3.07
   5 A-T      3.53     -5.05     36.82      3.14
   6 A-T      3.32     -5.83     32.80      3.09
   7 T-A      2.98     -6.44     34.14      3.23
   8 T-A      2.99     -7.13     39.93      2.82
   9 C-G      2.88     -4.95     29.46      4.19
  10 G-C      2.34     -6.66     39.85      2.81
  11 C-G      2.37    -10.68     35.99      3.90
  12 G-C      1.85     -4.90      ---       ---

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