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Author Topic: Uncalculated step-parameters angles with ANALYZE  (Read 4092 times)

Offline ns_rodriguezm

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Uncalculated step-parameters angles with ANALYZE
« on: September 13, 2016, 02:59:29 pm »
Dear Xiang-Ju,

I'm currently having problems with 3DNA for calculating some DNA step-angles (I'm interest in Tilt, Roll and Twist specifically) with the analyze command.
The structure that's currently giving me problems is 3O62 (PDB ID), is a nucleosome structure and I'm using only the DNA 3D information in the PDB file.

To give some context... Because of the distortions due to the curvature, the pairs that find_pair's command assings are not the ones that I expected and needed to work with (I'm comparing parameters that read the sequence of the nucleosomes with others that calculate based on the structure, that's why I need to be reading the same basepairs in the structure as those from the sequence).  In this case the pairs weren't assigned as I needed by find_pair's output so after reading some comments in this blog I decided to manually edit the find_pair's output to add or correct the missing/mistaken pairs.

This is an example with an extract from the output where my actual problem is, the possition 7 is the one I added:

prob_3O62_9nuc.pdb
corr_prob_3O62_9nuc.out
    2         # duplex
   10         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   20  0 #    1 | ....>I:..46_:[.DG]G-----C[.DC]:.101_:J<....  0.16  0.13 10.81  9.11 -4.04
    2   19  0 #    2 | ....>I:..47_:[.DC]C-----G[.DG]:.100_:J<....  2.27  2.12  6.04  8.60  1.81
    3   18  0 #    3 | ....>I:..48_:[.DT]T-----A[.DA]:..99_:J<....  0.64  0.55 37.77  9.28 -1.38
    4   17  0 #    4 | ....>I:..49_:[.DC]C-----G[.DG]:..98_:J<....  0.24  0.12  3.39  9.03 -4.35
    5   16  0 #    5 | ....>I:..50_:[.DC]C-----G[.DG]:..97_:J<....  0.18  0.15 11.89  9.13 -3.93
    6   15  9 #    6 | ....>I:..51_:[.DA]A-----T[.DT]:..96_:J<....  0.48  0.45 22.85  8.84 -2.47
    7   14  9 #    7 | ....>I:..52_:[.DT]T-----A[.DA]:..95_:J<....
    8   13  0 #    8 | ....>I:..53_:[.DC]C-----G[.DG]:..94_:J<....  0.40  0.38  6.10  9.17 -3.53
    9   12  0 #    9 | ....>I:..54_:[.DA]A-----T[.DT]:..93_:J<....  0.72  0.70 27.02  8.94 -1.54
   10   11  0 #   10 | ....>I:..55_:[.DA]A-----T[.DT]:..92_:J<....  0.21  0.14 26.31  8.94 -3.19
##### 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 (6): 1 - 6
##### Helix #2 (3): 7 - 9


After this I used this output as an input for analyze, having this as result for the secction with the angles I'm interest in:

****************************************************************************
Local base-pair step parameters
    step       Shift     Slide      Rise      Tilt      Roll     Twist
   1 GC/GC      0.03     -0.47      3.84    -16.09     -2.17     26.31
   2 CT/AG     -2.53      0.16      3.10      7.93    -18.96     41.74
   3 TC/GA      3.00      0.96      3.41     13.99    -15.58     41.10
   4 CC/GG     -0.26      0.11      3.11     -2.39      5.33     39.85
   5 CA/TG      1.21      1.17      3.23     10.28      2.31     38.36
   6 AT/AT      ----      ----      ----      ----      ----      ----
   7 TC/GA      ----      ----      ----      ----      ----      ----
   8 CA/TG      0.02     -1.15      3.60      2.26     19.11     30.31
   9 AA/TT     -1.11      0.75      2.84    -11.59      2.26     44.65
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      ave.      0.05      0.22      3.31      0.63     -1.10     37.47
      s.d.      1.74      0.83      0.34     11.30     12.93      6.65
****************************************************************************



Here you can see that the position 6 and 7 have missing angles that the program doesn't calculate. I haven't found a reason for that:
-There are other positions more distorted than this one where analyze calculates the angles
-I've edited other find_pair's outputs and it didn't generate any problems
-Checking the PDB file for this bases there is no apparent problem with missing atoms or others
-I've tried using analyze -c1 with no better result

I hope this is clear enough.

Glad to hear any suggestions.

Thanks a lot,

Natalia.


PS: in the attachment is the PDB file for the portion of the structure that I'm using as an example here.

Offline xiangjun

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Re: Uncalculated step-parameters angles with ANALYZE
« Reply #1 on: September 13, 2016, 05:19:21 pm »
Hi Natalia,

Thanks for using 3DNA and posting your questions on the Forum.

Briefly speaking, using the -c option would make analyze output the the missing parameters you need. Let's call the modified input file "corr_bps.txt", try the following command:

Code: [Select]
analyze -c corr_bps.txt
You will get:

Code: [Select]
****************************************************************************
Local base-pair step parameters
    step       Shift     Slide      Rise      Tilt      Roll     Twist
   1 GC/GC      0.03     -0.47      3.84    -16.09     -2.17     26.31
   2 CT/AG     -2.53      0.16      3.10      7.93    -18.96     41.74
   3 TC/GA      3.00      0.96      3.41     13.99    -15.58     41.10
   4 CC/GG     -0.26      0.11      3.11     -2.39      5.33     39.85
   5 CA/TG      1.21      1.17      3.23     10.28      2.31     38.36
   6 AT/AT     -2.23     -0.63      3.90     10.40      4.32     30.75
   7 TC/GA      2.36     -0.53      4.75    -13.03     17.32     32.13
   8 CA/TG      0.02     -1.15      3.60      2.26     19.11     30.31
   9 AA/TT     -1.11      0.75      2.84    -11.59      2.26     44.65
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       ave.      0.05      0.04      3.53      0.20      1.55     36.13
       s.d.      1.89      0.80      0.58     11.43     12.79      6.35

I am impressed by the efforts you put into solving the problems yourself. Clearly, the documentation needs to be improved in cases like this. The command-line help message with -c is as below,

Code: [Select]
        -c      output structural parameters between helical regions
                ("----" by default). The same effect can be achieved by
                directly modifying the input file (change "9" or "1" to
                "0" in the third column of each base pair list.)

What'd you suggest to make the documentation more obvious?

Best regards,

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.