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Topics - ns_rodriguezm

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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.

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Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University