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91
FAQs / Re: How to fix missing (superfluous) base pairs identified by find_pair?
« Last post by xiangjun on January 03, 2018, 10:59:04 am »
Hi,

Thanks for your followup. I sort of understand your confusions in general. Your case could serve as an excellent example to clarify some subtle points in 3DNA. To proceed, could you please provide details what you did, especially how you generate the attached image?

Best regards,

Xiang-Jun
92
FAQs / Re: How to fix missing (superfluous) base pairs identified by find_pair?
« Last post by sli on January 03, 2018, 02:29:58 am »
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!


 
93
FAQs / Re: How to fix missing (superfluous) base pairs identified by find_pair?
« Last post by xiangjun on January 02, 2018, 10:33:09 am »
In your my.pdb structure, the DNA nucleotide D.UF2/17 is flipped out of the duplex, instead of forming a pair with C.DG12. In such cases, you could proceed as noted in the FAQ:

Quote
In addition to (or instead of) manipulating parameters in misc_3dna.par, oftentimes it may be preferable to manually edit find_pair-generated base-piar files before feeding them into analyze/cehs. This allows for maximum flexibility as to which pair to consider in calculating 3DNA structural parameters.

So you could manually edit the find_pair output: changing 27 to 28, and add an extra line "209 242" as highlighted in red below. Note that in such cases, the step parameters (such as slide/roll etc) may not make intuitive sense (the numbers look weird). Nevertheless, they can be used to rigorously "rebuild" the original base geometry. See the 2008 3DNA Nature Protocols paper for more info.

my.pdb
my.out
    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   0 #   11 x ....>C:..11_:[.DC]C-----G[.DG]:..18_:D<....   0.35   0.30  19.14   8.92  -3.08
  209   242   0
  210   241   0 #   12 | ....>C:..13_:[.DT]T-----A[.DA]:..16_:D<....   0.29   0.11  18.66   8.94  -3.55

  211   240   0 #   13 | ....>C:..14_:[.DG]G-----C[.DC]:..15_:D<....   0.18   0.13  10.54   9.00  -4.03
  212   239   0 #   14 | ....>C:..15_:[.DA]A-----T[.DT]:..14_:D<....   0.48   0.02   7.98   8.84  -4.09
  213   238   0 #   15 | ....>C:..16_:[.DG]G-----C[.DC]:..13_:D<....   0.29   0.21   8.86   9.02  -3.85
  214   237   0 #   16 | ....>C:..17_:[.DC]C-----G[.DG]:..12_:D<....   0.39   0.09  11.91   8.95  -3.84
  215   236   0 #   17 | ....>C:..18_:[.DG]G-----C[.DC]:..11_:D<....   0.46   0.11  16.51   8.89  -3.50
  216   235   0 #   18 | ....>C:..19_:[.DA]A-----T[.DT]:..10_:D<....   0.23   0.20  15.04   8.89  -3.62
  217   234   0 #   19 | ....>C:..20_:[.DT]T-----A[.DA]:...9_:D<....   0.12   0.02  13.95   8.86  -4.15
  218   233   0 #   20 | ....>C:..21_:[.DG]G-----C[.DC]:...8_:D<....   0.27   0.03   4.95   8.88  -4.43
  219   232   0 #   21 | ....>C:..22_:[.DG]G-----C[.DC]:...7_:D<....   0.36   0.19  14.07   8.97  -3.55
  220   231   0 #   22 | ....>C:..23_:[.DA]A-----T[.DT]:...6_:D<....   0.11   0.03  11.03   9.00  -4.27
  221   230   0 #   23 | ....>C:..24_:[.DC]C-----G[.DG]:...5_:D<....   0.26   0.01   5.16   9.01  -4.46
  222   229   0 #   24 | ....>C:..25_:[.DA]A-----T[.DT]:...4_:D<....   0.12   0.08  11.88   8.99  -4.13
  223   228   0 #   25 | ....>C:..26_:[.DG]G-----C[.DC]:...3_:D<....   0.19   0.10  12.55   9.07  -3.98
  224   227   0 #   26 | ....>C:..27_:[.DC]C-----G[.DG]:...2_:D<....   0.70   0.08  13.79   8.87  -3.45
  225   226   0 #   27 | ....>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
94
FAQs / some questions about find_pair?
« Last post by sli 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!
95
General discussions (Q&As) / Re: Problems using 'Analyze'
« Last post by xiangjun on December 23, 2017, 09:42:01 am »
Hi Ellia,

You need to run "find_pair" first to prepare pairing info for "analyze" to work out the parameters, as shown in the command-line help message:

Code: [Select]
INPUT
        given a PDB file "sample.pdb", the input to analyze can be most
        conveniently generated with the utility program find_pair:
        find_pair sample.pdb sample.inp
        an explicit input file (including 'stdin') must be specified.
EXAMPLES
        analyze sample.inp
        analyze sample1.inp sample2.inp sample3.inp
        find_pair sample.pdb stdout | analyze stdin
        find_pair sample.pdb stdout | analyze -c stdin

In other words, this is a two-step process. Using 355d as an example, you need to do the following:

Code: [Select]
find_pair 355d.pdb 355d.inp
analyze 355d.inp

HTH,

Xiang-Jun
96
General discussions (Q&As) / Problems using 'Analyze'
« Last post by Ellaliv on December 23, 2017, 06:09:55 am »
Hello,

I've downloaded and installed 3DNA and "played" with it a while to understand the basic commands and functions, using the manual given in the forum. I didn't encounter any problems.
In the past days the 'analyze' command has not been working as it used to for me.
I thought it was something wrong with my PDB input files but when I tried it on one of the PDB's from the examples directory I got the same error-

......Processing structure #1: <..\examples\analyze_rebuild\355d.pdb>......
cannot read strand information

What can I do to fix it and make it work again?

Thanks a lot in advance,
Ella.
97
Quote
I checked the software on ~5500 PDB entries and found that the fixed version of DSSR works correctly.

Glad to hear that!

In retrospect, the original goal was just to having a unique key for each chain in the JSON output. So when two chains already have different identifiers, as in the case for chains E (in model #1) and I (in model #2) in 4ilm.pdb2, the corresponding model numbers were excluded, for simplicity. I did not expect the key itself would be used/useful. With a specific use case, the inconsistency in keys of different model/chains was easily fixed.

For other viewers of this thread, if you find any inconsistency or just feel something is missing/not right with DSSR, please do not hesitate to let me know. By reporting DSSR-related issues on the Forum, you're likely to receive a quick fix to proceed with your project, and you help improve the software per se that would benefit the community at large.

Best regards,

Xiang-Jun
98
Sorry for delayed reply, but I checked the software on ~5500 PDB entries and found that the fixed version of DSSR works correctly.

Thank you very much for fast update.
99
I've updated DSSR so that the model number will be included in the key to identify a chain, with the --json option. So for 4ilm.pdb2, the two chains (E on model 1, and I on model 2) will be identified as m1_chain_E and m2_chain_I respectively.

See the updated output below for 4ilm.pdb2:

Code: [Select]
# x3dna-dssr -i=4ilm.pdb2 --symm --json | jq .chains
{
  "m1_chain_E": {
    "num_nts": 16,
    "bseq": "GCUAAUCUACUAUAGA",
    "sstr": "......((.....)).",
    "form": "A.....A......AA-",
    "helical_rise": 0.115,
    "helical_rise_std": 3.392,
    "helical_axis": [
      -0.734,
      -0.496,
      -0.464
    ],
    "point1": [
      64.548,
      -24.513,
      89.342
    ],
    "point2": [
      62.86,
      -25.653,
      88.275
    ],
    "num_chars": 46,
    "suite": "G!!C!!U!!A!!A4bU4nC1aU!!A!!C4pU2[A6pU!!A1aG1aA"
  },
  "m2_chain_I": {
    "num_nts": 16,
    "bseq": "GCUAAUCUACUAUAGA",
    "sstr": "......((.....)).",
    "form": "A....BA......A.-",
    "helical_rise": 0.305,
    "helical_rise_std": 3.547,
    "helical_axis": [
      0.584,
      0.616,
      0.528
    ],
    "point1": [
      79.844,
      -52.783,
      70.422
    ],
    "point2": [
      83.132,
      -49.316,
      73.395
    ],
    "num_chars": 46,
    "suite": "G!!C!!U!!A!!A!!U4nC1aU!!A!!C4pU2[A6pU2aA1aG!!A"
  }
}

Please verify that the update solves the inconsistency issue you have.

Best regards,

Xiang-Jun
100
Good catch, and your detailed report is exemplary. I’ll look into the issue and get back to you on the Forum, probably by tonight.

Thanks,

Xiang-Jun
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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.