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Messages - sli

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1
Thanks for your help and your suggestions!

2
Dear Dr. Lu,

         I am sorry I have not reply you on time. The above image generation process can be obtained from my attached file.

Best wishes!

3
Thank you very much! I add a line as following:
    2         # duplex
   28         # number of base-pairs
    1     1    # explicit bp numbering/hetero atoms
  198   253   0 #    1 | ....>C:...1_:[.DC]C-----G[.DG]:..28_:D<....   0.09   0.00  12.58   9.13  -4.27
  199   252   0 #    2 | ....>C:...2_:[.DA]A-----T[.DT]:..27_:D<....   0.29   0.11  12.49   8.76  -3.87
  200   251   0 #    3 | ....>C:...3_:[.DG]G-----C[.DC]:..26_:D<....   0.38   0.17  11.55   8.98  -3.71
  201   250   0 #    4 | ....>C:...4_:[.DC]C-----G[.DG]:..25_:D<....   1.05   0.36  15.27   8.77  -2.47
  202   249   0 #    5 | ....>C:...5_:[.DT]T-----A[.DA]:..24_:D<....   0.18   0.01  12.00   8.93  -4.21
  203   248   0 #    6 | ....>C:...6_:[.DC]C-----G[.DG]:..23_:D<....   0.19   0.02   9.73   9.01  -4.29
  204   247   0 #    7 | ....>C:...7_:[.DT]T-----A[.DA]:..22_:D<....   0.28   0.04   8.95   9.03  -4.18
  205   246   0 #    8 | ....>C:...8_:[.DG]G-----C[.DC]:..21_:D<....   0.34   0.08   7.51   8.96  -4.12
  206   245   0 #    9 | ....>C:...9_:[.DT]T-----A[.DA]:..20_:D<....   0.20   0.12   8.73   8.88  -4.12
  207   244   0 #   10 | ....>C:..10_:[.DA]A-----T[.DT]:..19_:D<....   0.23   0.18  13.22   8.78  -3.75
  208   243   9 #   11 x ....>C:..11_:[.DC]C-----G[.DG]:..18_:D<....   0.35   0.30  19.14   8.92  -3.08
  209   242   0 #   12 | ....>C:..12_:[.DG]G-----UF2[.DUF2]:..17_:D<....
  210   241   0 #   13 | ....>C:..13_:[.DT]T-----A[.DA]:..16_:D<....   0.29   0.11  18.66   8.94  -3.55
  211   240   0 #   14 | ....>C:..14_:[.DG]G-----C[.DC]:..15_:D<....   0.18   0.13  10.54   9.00  -4.03
  212   239   0 #   15 | ....>C:..15_:[.DA]A-----T[.DT]:..14_:D<....   0.48   0.02   7.98   8.84  -4.09
  213   238   0 #   16 | ....>C:..16_:[.DG]G-----C[.DC]:..13_:D<....   0.29   0.21   8.86   9.02  -3.85
  214   237   0 #   17 | ....>C:..17_:[.DC]C-----G[.DG]:..12_:D<....   0.39   0.09  11.91   8.95  -3.84
  215   236   0 #   18 | ....>C:..18_:[.DG]G-----C[.DC]:..11_:D<....   0.46   0.11  16.51   8.89  -3.50
  216   235   0 #   19 | ....>C:..19_:[.DA]A-----T[.DT]:..10_:D<....   0.23   0.20  15.04   8.89  -3.62
  217   234   0 #   20 | ....>C:..20_:[.DT]T-----A[.DA]:...9_:D<....   0.12   0.02  13.95   8.86  -4.15
  218   233   0 #   21 | ....>C:..21_:[.DG]G-----C[.DC]:...8_:D<....   0.27   0.03   4.95   8.88  -4.43
  219   232   0 #   22 | ....>C:..22_:[.DG]G-----C[.DC]:...7_:D<....   0.36   0.19  14.07   8.97  -3.55
  220   231   0 #   23 | ....>C:..23_:[.DA]A-----T[.DT]:...6_:D<....   0.11   0.03  11.03   9.00  -4.27
  221   230   0 #   24 | ....>C:..24_:[.DC]C-----G[.DG]:...5_:D<....   0.26   0.01   5.16   9.01  -4.46
  222   229   0 #   25 | ....>C:..25_:[.DA]A-----T[.DT]:...4_:D<....   0.12   0.08  11.88   8.99  -4.13
  223   228   0 #   26 | ....>C:..26_:[.DG]G-----C[.DC]:...3_:D<....   0.19   0.10  12.55   9.07  -3.98
  224   227   0 #   27 | ....>C:..27_:[.DC]C-----G[.DG]:...2_:D<....   0.70   0.08  13.79   8.87  -3.45
  225   226   0 #   28 | ....>C:..28_:[.DT]T-----A[.DA]:...1_:D<....   0.32   0.23  16.73   8.85  -3.38
##### Base-pair criteria used:     4.00     0.00    15.00     2.50    65.00     4.50     7.80 [ O N]
##### 0 non-Watson-Crick base-pairs, and 2 helices (0 isolated bps)
##### Helix #1 (11): 1 - 11
##### Helix #2 (16): 12 - 27

I found that on the line I added, the result of the output file(be_step.par) was the same whether I add the number(like as 0.30   0.35  18.14   9.92  -3.33 ) or not. and then I use the modified file(my.bps) to "analyze" and finally "rebuild" DNA structure.In addition, I align the original DNA structure and the rebuild DNA structure by Pymol(pair_fit) ,they are not completely same. So I am not sure that my rebuild structure is right. Because I can not well understand means of your words:"Nevertheless, they can be used to rigorously "rebuild" the original base geometry". Is it said that the rebuild structure should completely as the original one? The aligned result is shown in the attachment.

Best wishes!


 

4
FAQs / some questions about find_pair?
« on: January 02, 2018, 02:01:25 am »
Dear Dr. Lu
        I want to get DNA structure's information  from a pdb file of DNA-protein complex.when I use 'find_pair' program , the mismatched base pairs which one base is completely flipping are default deleted.  My object is collect the size of the roll angle of the mismatched base pair. Due to my.bps file is lack of the mismatched base pair,when I use 'analyze my.bps' to generate 'bp_step.par', there are not  the mismatched base pairs information. I referenced the method of ' How to fix missing (superfluous) base pairs identified by find_pair?'  .But I still  not solve my problem. Could you give me some suggestions? Thank you!

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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.