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Hi Xiang-Jun
I am calculating the structures with QM and thinking to calculate the struc.parameters with 3DNA for some stacking base-pairs.I first use 3DNA and encounter with a trouble on how the cartesian coordinates transform to PDB format.I don't know how to get aroud of this problem. Can you help me?
Regarts
Si-Ya
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Hi Si-Ya,
In the manual of 3DNA, the calculation going from atomic coordinates to helix parameter frame is discussed quite thoroughly.
Further there are some references, which discuss this in more detail. Since I don't have the manual lying around here.....
There is a paper by Babcock et al.. which discusses a couple of parameters, and than there is a paper by Calladine et al (I think), which has quite a "simple" approach for some of the helix parameters.
Sorry I cannot be more specific. If I have the time, I'll look up the references and write them down here.
Unfortunately, it is not a type-and-go solution.
If you have analytical expressions for these transformations, I'd be happy to hear them.
Kind regards,
Ramon van der Werf
Radboud University Nijmegen, The Netherlands
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Hi Ramon,
Thank you in advance for your help.
I hope that the dates of stacking base-pair structure are transformed from the cartesian coordinate to PDB format so as to calculating base-pair steps parameter
I don't know how to solve it. Please help me.
Kind regards,
Si-Ya
The dates of stacking base-pair structure appendix:
1 N -4.547 1.251 -3.596
2 C -3.321 0.564 -3.608
3 N -2.143 1.240 -3.607
4 C -2.177 2.555 -3.597
5 C -3.377 3.312 -3.596
6 C -4.547 2.624 -3.596
7 N -1.027 3.163 -3.598
8 H -0.990 4.166 -3.582
9 H -0.189 2.592 -3.584
10 O -3.251 -0.665 -3.598
11 H -5.404 0.739 -3.643
12 H -5.492 3.154 -3.615
13 N -3.902 -1.748 -0.377
14 C -2.508 -1.582 -0.356
15 N -1.953 -0.346 -0.275
16 C -2.757 0.696 -0.223
17 C -4.173 0.604 -0.257
18 C -4.711 -0.641 -0.327
19 N -2.185 1.865 -0.159
20 H -2.747 2.695 -0.111
21 H -1.172 1.893 -0.117
22 O -1.728 -2.533 -0.396
23 H -4.294 -2.661 -0.487
25 H -4.815 1.469 -0.229
24 H -5.785 -0.773 -0.364
26 N 0.653 -0.820 2.976
27 C 1.276 -2.015 2.857
28 N 0.658 -3.190 2.759
29 C -0.706 -3.078 2.789
30 C -1.438 -1.912 2.912
31 C -0.717 -0.667 3.004
32 O -1.151 0.480 3.109
33 H 1.212 0.017 3.059
34 H 3.093 -1.126 2.934
35 H 3.057 -2.883 2.788
36 H -1.429 -5.070 2.558
37 H -3.684 -3.922 2.802
38 N -2.812 -2.192 2.936
39 C -2.854 -3.494 2.829
40 N 4.230 2.788 3.359
41 C 3.633 4.008 3.544
42 C 2.280 4.108 3.616
43 C 1.532 2.910 3.475
44 N 0.232 2.947 3.540
45 N 2.076 1.725 3.297
46 C 3.429 1.640 3.237
47 O 3.904 0.518 3.059
48 H 4.256 4.885 3.651
49 H 1.819 5.070 3.775
50 H -0.272 2.076 3.412
51 H -0.238 3.824 3.668
52 N 4.956 0.181 -0.223
53 C 4.986 1.551 -0.144
54 N 3.813 2.120 -0.061
55 C 2.925 1.037 -0.121
56 C 1.486 0.981 -0.093
57 O 0.670 1.899 0.015
58 N 0.979 -0.295 -0.215
59 C 1.750 -1.403 -0.333
60 N 1.127 -2.542 -0.449
61 N 3.080 -1.407 -0.353
62 C 3.617 -0.154 -0.240
63 H 5.785 2.246 -0.078
64 H -0.026 -0.395 -0.223
65 H 0.110 -2.587 -0.440
66 H 1.684 -3.373 -0.551
67 N 3.772 -2.376 -3.698
68 C 4.600 -1.280 -3.689
69 N 3.979 -0.131 -3.638
70 C 2.625 -0.495 -3.625
71 C 1.426 0.301 -3.550
72 O 1.308 1.522 -3.472
73 N 0.266 -0.445 -3.554
74 C 0.240 -1.798 -3.622
75 N -0.935 -2.363 -3.650
76 N 1.317 -2.577 -3.696
77 C 2.488 -1.868 -3.682
78 H 5.546 -1.057 -3.775
79 H -0.609 0.058 -3.514
80 H -1.782 -1.800 -3.614
81 H -0.973 -3.364 -3.722
82 H 5.226 2.701 3.368
83 H 4.026 -3.343 -3.679
84 N 2.579 -2.002 2.855
85 N -1.629 -4.101 2.706
86 H -3.385 4.391 -3.604
87 H 5.727 -0.456 -0.240
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First, thanks to Ramon for getting actively involved in answering other user's question. Over the years, it is my hope that 3DNA forum could turn into a virtual community where more people would participate in discussing issues related to nucleic acid structures. I am hoping others will follow your lead, and the 3DNA forum becomes more active.
Now to Si-Ya's question. 3DNA starts from a nucleic-acid containing structure in PDB format (http://www.wwpdb.org/documentation/format32/v3.2.html). Note specifically the coordinate section (http://www.wwpdb.org/documentation/format32/sect9.html). As a more concrete example, have a look of the residue DT8 in chain A of entry 355d, as shown below:
ATOM 142 P DT A 8 5.196 18.285 8.120 1.00 13.16 P
ATOM 143 OP1 DT A 8 3.928 18.831 8.653 1.00 14.21 O
ATOM 144 OP2 DT A 8 5.211 16.970 7.475 1.00 12.40 O
ATOM 145 O5' DT A 8 5.818 19.323 7.094 1.00 12.21 O
ATOM 146 C5' DT A 8 6.104 20.657 7.510 1.00 10.87 C
ATOM 147 C4' DT A 8 6.937 21.347 6.466 1.00 9.09 C
ATOM 148 O4' DT A 8 8.271 20.815 6.382 1.00 8.32 O
ATOM 149 C3' DT A 8 6.372 21.324 5.049 1.00 9.83 C
ATOM 150 O3' DT A 8 6.060 22.664 4.718 1.00 11.88 O
ATOM 151 C2' DT A 8 7.476 20.700 4.203 1.00 8.59 C
ATOM 152 C1' DT A 8 8.709 20.942 5.040 1.00 7.33 C
ATOM 153 N1 DT A 8 9.786 19.985 4.858 1.00 7.74 N
ATOM 154 C2 DT A 8 11.028 20.464 4.498 1.00 6.25 C
ATOM 155 O2 DT A 8 11.253 21.654 4.285 1.00 7.74 O
ATOM 156 N3 DT A 8 12.003 19.496 4.402 1.00 6.29 N
ATOM 157 C4 DT A 8 11.852 18.139 4.631 1.00 5.16 C
ATOM 158 O4 DT A 8 12.819 17.406 4.547 1.00 6.98 O
ATOM 159 C5 DT A 8 10.502 17.708 4.979 1.00 5.39 C
ATOM 160 C7 DT A 8 10.230 16.254 5.214 1.00 6.78 C
ATOM 161 C6 DT A 8 9.556 18.638 5.074 1.00 5.19 C
It is not just about the coordinates, but also about the naming convention of the base and backbone atoms. For example, for thymine, you have N1--C2--N3--C4--C5--C6 ring atoms, and O2 and O4 atoms attaching to C2 and C4.
As your example shows, it is clearly not in proper PDB format. It seems to be in xyz format. One might consider using 'babel' to convert it into PDB format. However, this converted version is not the one accepted by 3DNA, for reasons detailed in the above paragraph. I vaguely remember there is some tool to do proper conversion to PDB with correct atom names. Google it to see for yourself. For your specific purpose, I guess the 'simplest' way is to write a script to perform the conversion by taking into atom name convention into consideration.
HTH,
Xiang-Jun
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Hi Si-Ya,
Looking at the reply from Xiang-Jun, I must have misunderstood your question.
I understood your question as how to implement transformation from helix parameter frame to cartesian coordinates.
This is described in the papers:
M.S. Babcock, E.P.D. Pednault, W.K. Olson (1994): J.Mol.Biol., 237(1), pp. 125-156
- Formal and correct, but takes some time to read
M.S. Babcock, E.P.D. Pednault, W.K. Olson (1995): J.Mol.Biol., 251(5), pp. 648-664
- Easily accessible, but some details are taken from the article I mentioned above
Now I understand you do use 3DNA for this task, but want to transform the 3DNA coordinate file to a proper PDB format.
In the past I have written scripts to convert 3DNA to a format that Xplor (Structure calculation program) can use.
Later I have written a script to convert from X-plor format to PDB format (which is accepted for submitting structures to the online protein databank).
Do you want to submit your structure to the online databank ? Or do you want to do further analysis requiring cartesian coordinates ?
But I think trying Openbabel is certainly worth a try, this is the easiest optin available. It can be obtained in some Linux distributions via the automatic update option (In Fedora Core 9+ as root: yum install openbabel). Otherwise it can be obtained via http://openbabel.org/wiki/Main_Page (http://openbabel.org/wiki/Main_Page).
I will look up these scripts (as soon as I booted into Linux again), and post them here. (Or if I have time, combine the two to one 3DNA2PDB script)
Regards,
Ramon van der Werf
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Attached you'll find the scripts I mentioned.
When you untar, i.e. tar -xvzf pythonscripts.tar.gz
you will get two scripts:
3dna2xplor.py
xplor2pdb.py
To convert a file from 3dna to xplor compatible format, type in the command line:
python 3dna2xplor.py
(Answer the questions it poses, and it will work. I don't know how it handles Thymidine residues)
Then you edit xplor2pdb.
line 8 gives the inputfile. (note: pdbbestand is dutch for pdb file)
line 9 gives the outputfile (This is the one to be written in TRUE PDB FORMAT)
Sorry for this confusing naming of variables.
During my Ph.D. I've written a dozen of scripts, and their not all as neat as they should be.
After editing the file, save and run from the command line:
python xplor2pdb.
In the output file the 'END' at the end of the PDB file has an empty space before it. This should be removed for submission.
Regards,
Ramon
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