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Questions and answers > w3DNA -- web interface to 3DNA
web-3DNA not running on some pdb entries
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anjali09:
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.
xiangjun:
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: ---# 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
--- End code ---
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
anjali09:
Ok..Thanks
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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.