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Author Topic: Problem in .Out file  (Read 3304 times)

Offline Anju Sharma

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Problem in .Out file
« on: June 15, 2007, 12:31:06 am »
hello sir
I carried simulations of DNA seq CGATCG alone using MOE s/w. when i converted the its .Pdb file into .Out file m getting only 3 base pairs
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Number of base-pairs: 3
Number of atoms: 246
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RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

            Strand I                    Strand II          Helix
   1   (0.049) -:...4_:[..T]T-*---G[..G]:...8_:- (0.090)     |
   2   (0.080) -:...3_:[..A]A-*---A[..A]:...9_:- (0.059)     |
   3   (0.077) -:...2_:[..G]G-*---T[..T]:..10_:- (0.036)     |

Note: This structure contains 3[0] non-Watson-Crick base-pairs.
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Can you pls explain me y m gettng diffrnt results.

Regards,

Anju Sharma
Anju Sharma,
Project Fellow,
NIT, Hamirpur,
Himachal Pradesh (India)

Offline xiangjun

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« Reply #1 on: June 15, 2007, 10:00:19 pm »
Firstly, please refer to a related post for background information.

More specifically, your DNA structures are too irregular to be recognized by "find_pair" as you would expect. The output file from "analyze" follows whatever base-pair information produced by "find_pair", and thus the "problems" your noticed. You could run "find_pair" to create an approximate starting input file and modify it accordingly as you see fit. The file format produced by "find_pair" is documented at the 3DNA homepage.

Also note that you can now add attachments to your post in this forum.

HTH,

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

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.