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Author Topic: web-3DNA not running on some pdb entries  (Read 928 times)

Offline anjali09

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web-3DNA not running on some pdb entries
« on: July 11, 2016, 11:12:02 am »
 I am using web-3DNA server for analyzing DNA helical parameters. I got the parameters for most PDB entries except 3FT6, 1G3X, 1VTH, 1VTI, 1JHI, 1DSD, 1FJA etc..
Kindly help me getting the parameters for these PDB entries.

Offline xiangjun

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Re: web-3DNA not running on some pdb entries
« Reply #1 on: July 11, 2016, 11:21:28 am »
Pending what Rutgers has to say about the web-3DNA server, you may try the command-line version of 3DNA. I've tried the current version (v2.3-2016apr02) on 3ft6 and 1fja, and all seem to run smoothly.

Code: [Select]
# excerpt from running "find_pair 3ft6.pdb | analyze"

****************************************************************************
Local base-pair parameters
     bp        Shear    Stretch   Stagger    Buckle  Propeller  Opening
    1 C-G       0.33     -0.24      0.35     -3.14    -14.04     -3.85
    2 G-C      -0.21     -0.18     -0.03     -4.14     -0.20     -3.38
    3 A-T       0.15     -0.13      0.09      0.89    -13.13      4.44
    4 T-A      -0.13     -0.13      0.09     -0.67    -13.11      4.25
    5 C-G       0.23     -0.19     -0.07      4.84     -0.27     -2.80
    6 G-C      -0.37     -0.25      0.35      3.41    -14.38     -3.89
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      ave.      0.00     -0.19      0.13      0.20     -9.19     -0.87
      s.d.      0.28      0.05      0.18      3.55      6.96      4.06
****************************************************************************
Local base-pair step parameters
    step       Shift     Slide      Rise      Tilt      Roll     Twist
   1 CG/CG      0.03      0.68      6.67      3.63      3.22     21.45
   2 GA/TC     -0.64      1.98      3.32     -6.47      7.80     36.56
   3 AT/AT     -0.01     -0.04      3.23     -0.05     -2.32     33.52
   4 TC/GA      0.67      2.00      3.32      6.80      7.37     36.38
   5 CG/CG     -0.03      0.68      6.67     -3.93      3.51     20.75
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       ave.      0.00      1.06      4.64     -0.00      3.92     29.73
       s.d.      0.46      0.90      1.85      5.41      4.08      7.97

So the issue is presumably to be related to an earlier version of 3DNA used by the web-3DNA server hosted at Rutgers.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline anjali09

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Re: web-3DNA not running on some pdb entries
« Reply #2 on: July 11, 2016, 11:35:21 am »
Ok..Thanks

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.