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Questions and answers => MD simulations => Topic started by: souviksur on April 17, 2012, 10:04:31 am

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Title: Analysis of PDB file:query
Post by: souviksur on April 17, 2012, 10:04:31 am

Dear all,

I am using 3DNA for analysis of data, but I found the output files were not proper, are the pdb files not appropriate or something else, please suggest me, I am attaching two pdb files with this mail, please find those in attachments and suggest me.

Souvik

Title: Re: Analysis of PDB file:query
Post by: xiangjun on April 17, 2012, 11:04:14 am

Quote

I found the output files were not proper

What do you mean "not proper"? What would you expect the output to be? I tried your attached PDB files, and found 3DNA is doing its job.

Xiang-Jun

Title: Re: Analysis of PDB file:query
Post by: souviksur on April 18, 2012, 12:36:09 am

there are 15 no.s of base pairs in each pdb, but I found in one case 9 and in another case 10 out of 15 pairs.

Title: Re: Analysis of PDB file:query
Post by: xiangjun on April 18, 2012, 09:33:32 am

Okay, let's check step-by-step how find_pair is working for your two attached structures.

The output for 30ns@mod_2.pdb is as you expected.

find_pair 30ns@mod_2.pdb 30ns@mod_2.bps
more 30ns@mod_2.bps
# the output is as below
30ns@mod_2.pdb
30ns@mod_2.out
    2         # duplex
   14         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   31  0 #    1 | ....>-:...1_:[DA5]a-**--t[TPN]:..31_:-<....  4.71  1.82 45.14  7.30  7.61
    2   30  0 #    2 | ....>-:...2_:[.DA]A-----t[TPN]:..30_:-<....  0.51  0.30 13.22  9.70 -3.24
    3   29  0 #    3 | ....>-:...3_:[.DT]T-----a[APN]:..29_:-<....  0.73  0.73  8.66  9.13 -2.38
    4   28  0 #    4 | ....>-:...4_:[.DT]T-----a[APN]:..28_:-<....  0.19  0.09 13.10  9.21 -3.98
    5   27  0 #    5 | ....>-:...5_:[.DT]T-----a[APN]:..27_:-<....  1.03  1.03 17.68  8.93  0.96
    6   26  0 #    6 | ....>-:...6_:[.DT]T-----a[APN]:..26_:-<....  0.23  0.22 16.23  9.13 -3.52
    7   25  0 #    7 | ....>-:...7_:[.DT]T-----a[APN]:..25_:-<....  0.37  0.36 10.91  8.99 -3.36
    8   24  0 #    8 | ....>-:...8_:[.DT]T-----a[APN]:..24_:-<....  0.30  0.01  9.28  9.21 -4.21
    9   23  0 #    9 | ....>-:...9_:[.DT]T-----a[APN]:..23_:-<....  0.49  0.12 10.87  9.24 -3.73
   10   22  0 #   10 | ....>-:..10_:[.DT]T-----a[APN]:..22_:-<....  0.18  0.05 14.36  8.97 -4.00
   11   21  0 #   11 | ....>-:..11_:[.DA]A-----t[TPN]:..21_:-<....  0.47  0.21  1.26  9.28 -4.05
   12   20  0 #   12 | ....>-:..12_:[.DT]T-----a[APN]:..20_:-<....  0.34  0.30  5.05  9.10 -3.80
   13   19  0 #   13 | ....>-:..13_:[.DT]T-----a[APN]:..19_:-<....  0.46  0.45 22.22  8.98 -2.53
   14   18  0 #   14 | ....>-:..14_:[.DT]T-----a[APN]:..18_:-<....  0.47  0.28 25.44  9.34 -2.71
##### Base-pair criteria used:     4.00     0.00    15.00     2.50    65.00     4.50     7.50 [ O N]
##### 1 non-Watson-Crick base-pair, and 1 helix (0 isolated bps)
##### Helix #1 (14): 1 - 14  ***broken O3' to P[i+1] linkage***

Using Jmol/PyMOL/RasMol to visualize the structure, one can easily verify that find_pair is behaving properly.

Now repeat the procedute for 30ns_nsp_mod.pdb, you'd get the following result which you thought as "improper":

find_pair 30ns_nsp_mod.pdb 30ns_nsp_mod.bps
more 30ns_nsp_mod.bps
# the output is as below
30ns_nsp_mod.pdb
30ns_nsp_mod.out
    2         # duplex
   10         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   31  0 #    1 | ....>-:...1_:[..A]A-**--T[..T]:..31_:-<....  6.27  0.03 22.42  9.06  6.46
    2   30  0 #    2 | ....>-:...2_:[..A]A-**--T[..T]:..30_:-<....  4.14  0.42 23.12  9.56  5.13
    3   29  0 #    3 | ....>-:...3_:[..T]T-----A[ADE]:..29_:-<....  0.13  0.01 20.45  9.45 -3.83
    4   28  0 #    4 | ....>-:...4_:[..T]T-----A[..A]:..28_:-<....  0.28  0.28 19.08  9.01 -3.21
    5   27  0 #    5 | ....>-:...5_:[..T]T-----A[..A]:..27_:-<....  0.40  0.11 18.15  9.35 -3.47
    6   26  0 #    6 | ....>-:...6_:[..T]T-----A[ADE]:..26_:-<....  0.64  0.51 27.99  9.05 -1.94
    7   25  9 #    7 x ....>-:...7_:[..T]T-----A[..A]:..25_:-<....  0.62  0.56 25.16  9.15 -2.00
   10   22  1 #    8 + ....>-:..10_:[..T]T-----A[..A]:..22_:-<....  0.64  0.53 15.83  9.01 -2.50
   13   19  0 #    9 | ....>-:..13_:[..T]T-----A[ADE]:..19_:-<....  0.48  0.19 18.51  5.17 -3.21
   14   18  0 #   10 | ....>-:..14_:[..T]T-----A[..A]:..18_:-<....  0.27  0.26 30.07  4.91 -2.71
##### Base-pair criteria used:     4.00     0.00    15.00     2.50    65.00     4.50     7.50 [ O N]
##### 2 non-Watson-Crick base-pairs, and 3 helices (1 isolated bp)
##### Helix #1 (7): 1 - 7  ***broken O3' to P[i+1] linkage***
##### Helix #2 (1): 8
##### Helix #3 (2): 9 - 10  ***broken O3' to P[i+1] linkage***

As shown in the image below, find_pair is again behaving as it should for this case. Is this structure itself what you'd expect?

(http://forum.x3dna.org/images/30ns_nsp_mod.png)

In my experience, whenever a user suspects the output from find_pair as "improper", it is more than likely that the structure itself is "weird" -- if in doubt, always check your structure using a molecular graphics visualization program (Jmol/PyMOL/RasMol etc). Of course, I am consistently on the watch to refine find_pair, especially for the edge cases.

Xiang-Jun

Title: Re: Analysis of PDB file:query
Post by: souviksur on April 19, 2012, 08:44:40 am

I modified the pds and now got 14 nos. of base pairs out of 15 ( I found there was some spacing problem in pdbs), thanks a lot, I am attaching the files.

Title: Re: Analysis of PDB file:query
Post by: xiangjun on April 19, 2012, 12:18:08 pm

Quote

now got 14 nos. of base pairs out of 15

There must be something special with the missing base pair. If you visualize the structure graphically using Jmol/PyMOL etc, I believe you won't take it as a "base pair" either. Checking the details why it is "missed" by find_pair would be an interesting exercise for those who want to understand 3DNA better.

Xiang-Jun

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.