base pair stagger

[auffinger]

Dear Xiang-Jun,

I am having a little problem with understanding your maximum vertical
distance between base origins since I was unable to find a description of
how these base origins are calculated. Could you give me a hint?

In fact, we realized that with the 2.5 criteria you propose we are taking
into account base pairs like the one attached to this mail (G-U pair) that
should obviously be excluded. The stagger value for this base pair is close
to 2.0 which is a quite high value. Could you also help me to find a
reference related to how this stagger parameter is caculated?

Pascal


REMARK    3DNA (v1.5, Nov. 2002) by Xiang-Jun Lu at Wilma K. Olson's Lab.
ATOM      1  P     G 0 257       4.449   6.613  -2.015  1.00 81.87           P  
ATOM      2  O5'   G 0 257       2.993   6.752  -1.388  1.00 80.67           O  
ATOM      3  C5'   G 0 257       2.072   7.748  -1.869  1.00 76.88           C  
ATOM      4  C4'   G 0 257       0.649   7.294  -1.649  1.00 74.57           C  
ATOM      5  O4'   G 0 257       0.487   5.980  -2.245  1.00 73.84           O  
ATOM      6  C3'   G 0 257       0.221   7.086  -0.203  1.00 72.87           C  
ATOM      7  O3'   G 0 257      -0.192   8.298   0.419  1.00 72.75           O  
ATOM      8  C2'   G 0 257      -0.937   6.119  -0.359  1.00 72.75           C  
ATOM      9  O2'   G 0 257      -2.113   6.758  -0.806  1.00 72.14           O  
ATOM     10  C1'   G 0 257      -0.405   5.206  -1.464  1.00 73.40           C  
ATOM     11  N9    G 0 257       0.326   4.070  -0.908  1.00 73.88           N  
ATOM     12  C8    G 0 257       1.684   3.842  -0.935  1.00 74.09           C  
ATOM     13  N7    G 0 257       2.029   2.744  -0.318  1.00 74.52           N  
ATOM     14  C5    G 0 257       0.829   2.211   0.136  1.00 73.68           C  
ATOM     15  C6    G 0 257       0.563   1.028   0.876  1.00 72.05           C  
ATOM     16  O6    G 0 257       1.363   0.187   1.294  1.00 72.32           O  
ATOM     17  N1    G 0 257      -0.797   0.873   1.122  1.00 70.92           N  
ATOM     18  C2    G 0 257      -1.780   1.742   0.715  1.00 71.57           C  
ATOM     19  N2    G 0 257      -3.039   1.429   1.056  1.00 70.83           N  
ATOM     20  N3    G 0 257      -1.547   2.843   0.026  1.00 72.99           N  
ATOM     21  C4    G 0 257      -0.232   3.014  -0.226  1.00 73.83           C  
ATOM     22  O1P   G 0 257       5.102   7.940  -1.901  1.00 82.54           O  
ATOM     23  O2P   G 0 257       5.112   5.414  -1.434  1.00 81.39           O  
ATOM     24  P     U 0 253      -4.704  -6.982  -0.337  1.00 65.64           P  
ATOM     25  O5'   U 0 253      -4.084  -5.768  -1.160  1.00 69.18           O  
ATOM     26  C5'   U 0 253      -4.932  -4.872  -1.903  1.00 73.30           C  
ATOM     27  C4'   U 0 253      -4.097  -3.875  -2.669  1.00 75.72           C  
ATOM     28  O4'   U 0 253      -3.480  -2.935  -1.751  1.00 75.82           O  
ATOM     29  C3'   U 0 253      -2.916  -4.450  -3.430  1.00 77.91           C  
ATOM     30  O3'   U 0 253      -3.273  -5.082  -4.654  1.00 79.93           O  
ATOM     31  C2'   U 0 253      -2.044  -3.218  -3.623  1.00 77.94           C  
ATOM     32  O2'   U 0 253      -2.524  -2.372  -4.648  1.00 78.00           O  
ATOM     33  C1'   U 0 253      -2.221  -2.528  -2.269  1.00 77.57           C  
ATOM     34  N1    U 0 253      -1.164  -2.892  -1.311  1.00 78.25           N  
ATOM     35  C2    U 0 253      -0.231  -1.923  -0.983  1.00 79.12           C  
ATOM     36  O2    U 0 253      -0.261  -0.790  -1.435  1.00 79.66           O  
ATOM     37  N3    U 0 253       0.745  -2.331  -0.105  1.00 79.61           N  
ATOM     38  C4    U 0 253       0.884  -3.576   0.465  1.00 79.00           C  
ATOM     39  O4    U 0 253       1.841  -3.800   1.210  1.00 79.06           O  
ATOM     40  C5    U 0 253      -0.124  -4.518   0.086  1.00 79.19           C  
ATOM     41  C6    U 0 253      -1.090  -4.153  -0.765  1.00 78.38           C  
ATOM     42  O1P   U 0 253      -5.725  -7.656  -1.182  1.00 64.76           O  
ATOM     43  O2P   U 0 253      -3.581  -7.769   0.226  1.00 65.63           O  
HETATM   44  O   HOH  4525       6.320   2.815  -0.315  1.00 66.90           O  
END

[xiangjun]

Hi Pascal,

Nice to communicate with you here.

The standard base reference frame is described in the Olson et al. (2001) JMB report. Specifically, the origin is defined as the center of what would a perfect Watson-Crick base-pair.

As detailed in the FAQ section of the current 3DNA homepage, the default set of parameters used in 3DNA was based on a survey of the NDB structures and is very generous to account for distorted bps. As an example, how much a H-bond distance cut-off should be choosen? Intuitively, 3.2 A would be a more reasonable value than 4.0 A. However, even with such high cut-off, some users still report "find_pair" missing some bps, which turns out that the shorted possible H-bond distance would be over 5.0 A in such bps.

That's exactly the reason that 3DNA provides the "misc_3dna.par" file for users to tune it for their specific purpose. For example, by setting d_org = 1.0, dv = 0.5, z_ang = 15, one will find only Watson-Crick base-pairs.

As far as how stagger parameter is calculated, it is the projection of the vector linking the two base origins onto the mean base z-axis. A step-by-step description of the procedure can be found in the 1997 JMB SCHNAaP paper. 3DNA uses exactly the same algorithm except for a change in reference frame.

HTH,

Xiang-Jun

[auffinger]

Hi Xiang-Jun,

I understand perfectly your point altough, personnally, I do think that using a h-bond distance above 3.5A is considerably exagerated, but that is an other topic.

Yes, I use the "misc_3dna.par" file. However, the aim of my question was to understand how you calulate this "vertical distance between base pair origins". Is this the same as this stagger parameter (probably not). Could you then tell me why you do not use the stagger parameter instead.

This is also why I wanted to know how you determine the "base origin". I already knew how you determine the "base pair origin".

Best regards,

Pascal

[xiangjun]

Hi Pascal,

The "dv" is the vertical distance between the two base planes -- it is actually stagger in magnitude (i.e., abs(stagger)).

Or it can be thought of as the "vertical distance between base pair origins" projected onto the mean normals of the two bases (z-axis of the bp).

The "base pair origin" is actually the geometric average of the two base origins. In 3DNA, starting from the standard base reference frame (Atomic_A.pdb etc), a least-squares fitting onto corresponding experimental base gives the base reference frame (i.e., its position [origin] and orientation [x-, y- and z-axis]).

A detailed step-by-step description of the ls-fitting procedure is provide at the 3DNA homepage technical details section. Please note that over there, the standard base coordinates used is not in the standard reference frame.

In 3DNA, you can get the output of the each base reference frame by:

Code: [Select]

find_pair -s PDB_FILE stdout | analyze
Then have a look of the file "ref_frames.dat".

HTH,

Xiang-Jun