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General discussions (Q&As) / 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.
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.