Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL
· Video Overview · DSSR v2.5.3 (DSSR Manual) · Homepage
-
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
-
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 (http://http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=9356255&query_hl=1&itool=pubmed_docsum). 3DNA uses exactly the same algorithm except for a change in reference frame.
HTH,
Xiang-Jun
-
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
-
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 (http://http://rutchem.rutgers.edu/~xiangjun/3DNA/tech_details.html). 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:
find_pair -s PDB_FILE stdout | analyze
Then have a look of the file "ref_frames.dat".
HTH,
Xiang-Jun
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