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Questions and answers > RNA structures (DSSR)
list nucleotide/nucleotide contacts involving a phosphate group.
auffinger:
Hi Xiang-Jun,
I was wondering if 3DNA provides (with some unknown options to me) a listing of the nucleotides that are linked by hydrogen bonds other than base-base ones.
For example, if two nucleotides interact by a single base/phosphate or a base/sugar or supar/phosphate contact, is there a way to get a list of them.
(of course this might involve specific hydrogen bond parameters).
Hope this is clear.
Best,
Pascal
xiangjun:
Hi Pascal,
Thanks for your request for adding non-pairing nucleotide-nucleotide contacts (nt-nt) in 3DNA output. Currently, there is no such an option in 3DNA, but I do have this topic in mind for quite a while. It won't be hard to implement this functionality in DSSR/3DNA, so I will probably be able to get something done next week.
While we are at it, in addition to non-pairing nt-nt interactions via H-bond, how about those with only base-stacking? What output format would be prefer?
Xiang-Jun
auffinger:
Hi Xiang-Jun,
Thanks for this quick reply.
I would be happy to try this out first for the non-base-base contacts.
Then of course stacking info would be great.
I suggest to add a stacking output file that would list stacking info in the usual way.
You will certainly find a good way to do that. I guess you would add info related to
the stacking of non-connected nucleotides. I am eager to see that.
Thanxs,
Pascal
xiangjun:
Hi Pascal,
I've just released DSSR beta-r09-on-20130421 which contains a new option -non-pair (or --non-pair) to detect/output non-pairing interactions, including H-bonds and base stacking. As an example, see below for PDB entry 1msy which contains a GNRA tetra-loop.
x3dna-dssr --non-pair -i=1msy -o=1msy.out
The output file '1msy.out' contains the following:
****************************************************************************
List of 12 non-pairing interaction(s)
1 A.G2648 A.G2673 base-overlap-area=2.0
H-bonds[0]: ""
2 A.U2650 A.G2671 base-overlap-area=0.1
H-bonds[0]: ""
3 A.C2652 A.G2669 base-overlap-area=0.2
H-bonds[0]: ""
4 A.A2654 A.U2656 base-overlap-area=3.7
H-bonds[1]: "O4'*O4'[3.05]"
5 A.G2655 A.G2664 base-overlap-area=4.4
H-bonds[1]: "O2'(hydroxyl)-O6(carbonyl)[3.09]"
6 A.G2655 A.A2665 base-overlap-area=0.0
H-bonds[3]: "N1(imino)-OP2[2.77]; N2(amino)-OP2[3.34]; N2(amino)-O5'[2.89]"
7 A.U2656 A.G2664 base-overlap-area=0.0
H-bonds[2]: "OP2-N1(imino)[3.04]; OP2-N2(amino)[2.94]"
8 A.A2657 A.A2665 base-overlap-area=3.7
H-bonds[0]: ""
9 A.G2659 A.A2661 base-overlap-area=0.0
H-bonds[1]: "O2'(hydroxyl)-N7[2.60]"
10 A.G2659 A.G2663 base-overlap-area=3.9
H-bonds[0]: ""
11 A.U2660 A.A2661 base-overlap-area=7.5
H-bonds[0]: ""
12 A.A2661 A.A2662 base-overlap-area=6.3
H-bonds[0]: ""
****************************************************************************
Please let me know how you'd like to revise the content/format. As always, concrete examples work the best.
Xiang-Jun
auffinger:
Hi Xiang-Jun,
Thats just great. It looks like a combined version of find_pair and analyze. Is that correct ?
Of course it seems not possible to (re)construct NA structures with DSSR.
So first, why calling it DSSR and not DSSNA since it works also for DNA ?
I think that one should avoid the RNA domination, it is possible to learn from both structures.
thus, does DSSR really work for DNA ?
____
Then, as for formats,
I think that as I mentioned it somewhere earlier, and since I am processing the output files
for a large number of structures, I appreciate when there are spacesbetween fields (see).
For exemple, in the dssr-torsion.dat file :
base_id alpha beta gamma delta epsilon zeta e-z chi phase-angle sugar-type Zp Dp
1 A.C2649 --- 167.1 47.6 84.1 -146.6 -77.1 -69(BI) -160.5(anti) 12.9(C3'-endo) ~C3'-endo 4.41 4.66
2 A.U2650 -64.2 164.2 60.3 79.8 -154.5 -73.1 -81(BI) -167.2(anti) 21.3(C3'-endo) ~C3'-endo 4.40 4.55
is easier to process if you write:
2 A.U2650 -64.2 164.2 60.3 79.8 -154.5 -73.1 -81 (BI) -167.2 (anti) 21.3 (C3'-endo) ~C3'-endo 4.40 4.55
and is there a need for writing twice the sugar pucker in this file ?
---
you name this file torsion although there are sugar puckers in it.
Thus it might be called torsion_puckers.dat or something else.
---
For the non-pairing interactions that is just a great feature,
you had before two values for base overlap
one calculated by just using ring atoms the other by using all base atoms.
you could add this.
---
Why adding the name of the chemical groups (hydroxyl, amino, imino, ...)
again this complicates reading since some groups are named and others not like OP2 and so on.
I would appreciate another presentation here.
___
I haven't really checked, but are your base pair numbering scheme coherent with the one
you use in find_pair ? It would be really nice to be the case.
___
Also, I wanted to ask you that but know it seems to be done. You add various names
to each base pair. Thats great. Just a hint to the various nomenclatures (Leontis-Westhof, Saenger...)
would be helpful in the *.out files.
---
is there a configuration file that would allow to precise hydrogen bond and other parameters like in 3DNA.
I would really appreciate that.
---
more later,
Tanks for the great work,
Pascal
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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.
