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Topics - shuxiang

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1
Hi Xiang-Jun,

I encounter a question when plotting separate frames for each base in a base pair. See the attached picture, each base has its own reference frame.


From the ref_frames.dat file, I get the information like following.  If I understand correctly, it looks like the reference frames here are the averaged frames for a base pair.
...     6 A-T   # A:...6_:[.DA]A - B:..19_:[.DT]T
   14.8825    20.6882    10.2718  # origin
    0.9873    -0.1230    -0.1006  # x-axis
   -0.0859    -0.9457     0.3135  # y-axis
   -0.1337    -0.3009    -0.9442  # z-axis

I want to obtain the reference frame for each base in a paired bases. Thank you.

Best,
Shuxiang

2
RNA structures (DSSR) / strange residue number after dssr --view option
« on: August 06, 2018, 01:10:13 pm »
Hi Xiang-Jun,

I'm using the following command to convert a DNA\protein structure into its best view conformation. (3mgp.cif is downloaded from PDB database).

x3dna-dssr -i=3mgp.cif -o=3mgp_view.cif --view

The weird thing is the residue number index of the DNA part from original file (3mgp.cif)  is from 1 to 147. However, the corresponding residue number index from best view file (3mgp_view.cif) is from -73 to 73. I'm wondering is there an opinion to keep the residue renumber same between the original file and dssr output file? Thank you. 

For example, the beginning DNA part of 3mgp.cif is:
ATOM   6161  O  "O5'" . DA  I  5 1   ? 2.638   0.163   93.308 1.00 166.52 ? -73  DA  I "O5'" 1
ATOM   6162  C  "C5'" . DA  I  5 1   ? 3.279   0.178   94.579 1.00 166.78 ? -73  DA  I "C5'" 1
ATOM   6163  C  "C4'" . DA  I  5 1   ? 3.645   -1.223  95.042 1.00 167.01 ? -73  DA  I "C4'" 1
ATOM   6164  O  "O4'" . DA  I  5 1   ? 2.489   -2.096  95.012 1.00 167.37 ? -73  DA  I "O4'" 1
ATOM   6165  C  "C3'" . DA  I  5 1   ? 4.650   -1.969  94.180 1.00 166.94 ? -73  DA  I "C3'" 1
ATOM   6166  O  "O3'" . DA  I  5 1   ? 5.972   -1.523  94.462 1.00 166.58 ? -73  DA  I "O3'" 1
ATOM   6167  C  "C2'" . DA  I  5 1   ? 4.428   -3.410  94.635 1.00 167.20 ? -73  DA  I "C2'" 1
ATOM   6168  C  "C1'" . DA  I  5 1   ? 2.941   -3.442  94.998 1.00 167.53 ? -73  DA  I "C1'" 1
ATOM   6169  N  N9    . DA  I  5 1   ? 2.097   -4.257  94.106 1.00 167.70 ? -73  DA  I N9    1
ATOM   6170  C  C8    . DA  I  5 1   ? 0.995   -3.832  93.410 1.00 167.66 ? -73  DA  I C8    1
ATOM   6171  N  N7    . DA  I  5 1   ? 0.415   -4.762  92.687 1.00 167.66 ? -73  DA  I N7    1
ATOM   6172  C  C5    . DA  I  5 1   ? 1.185   -5.889  92.920 1.00 167.82 ? -73  DA  I C5    1
ATOM   6173  C  C6    . DA  I  5 1   ? 1.094   -7.219  92.443 1.00 167.68 ? -73  DA  I C6    1
ATOM   6174  N  N6    . DA  I  5 1   ? 0.141   -7.629  91.598 1.00 167.61 ? -73  DA  I N6    1
ATOM   6175  N  N1    . DA  I  5 1   ? 2.020   -8.112  92.866 1.00 167.60 ? -73  DA  I N1    1
ATOM   6176  C  C2    . DA  I  5 1   ? 2.972   -7.698  93.715 1.00 167.61 ? -73  DA  I C2    1
ATOM   6177  N  N3    . DA  I  5 1   ? 3.161   -6.478  94.229 1.00 167.74 ? -73  DA  I N3    1
ATOM   6178  C  C4    . DA  I  5 1   ? 2.227   -5.603  93.793 1.00 167.85 ? -73  DA  I C4    1
ATOM   6179  P  P     . DT  I  5 2   ? 6.808   -0.641  93.411 1.00 166.33 ? -72  DT  I P     1
ATOM   6180  O  OP1   . DT  I  5 2   ? 6.500   0.779   93.692 1.00 166.34 ? -72  DT  I OP1   1
ATOM   6181  O  OP2   . DT  I  5 2   ? 6.588   -1.186  92.052 1.00 166.28 ? -72  DT  I OP2   1
ATOM   6182  O  "O5'" . DT  I  5 2   ? 8.341   -0.918  93.788 1.00 165.73 ? -72  DT  I "O5'" 1
ATOM   6183  C  "C5'" . DT  I  5 2   ? 8.715   -1.557  95.009 1.00 164.98 ? -72  DT  I "C5'" 1
ATOM   6184  C  "C4'" . DT  I  5 2   ? 9.072   -3.018  94.786 1.00 164.44 ? -72  DT  I "C4'" 1
ATOM   6185  O  "O4'" . DT  I  5 2   ? 7.900   -3.772  94.389 1.00 164.50 ? -72  DT  I "O4'" 1
ATOM   6186  C  "C3'" . DT  I  5 2   ? 10.122  -3.278  93.711 1.00 164.05 ? -72  DT  I "C3'" 1
ATOM   6187  O  "O3'" . DT  I  5 2   ? 11.270  -3.824  94.345 1.00 163.49 ? -72  DT  I "O3'" 1
ATOM   6188  C  "C2'" . DT  I  5 2   ? 9.469   -4.258  92.730 1.00 164.06 ? -72  DT  I "C2'" 1
ATOM   6189  C  "C1'" . DT  I  5 2   ? 8.302   -4.824  93.535 1.00 164.11 ? -72  DT  I "C1'" 1

The beginning DNA part of 3mgp_view.cif is:
ATOM   6161  O5'  DA I -73     -44.102 -28.116  24.446  1.00166.52           O
ATOM   6162  C5'  DA I -73     -45.300 -28.880  24.535  1.00166.78           C
ATOM   6163  C4'  DA I -73     -45.873 -29.191  23.161  1.00167.01           C
ATOM   6164  O4'  DA I -73     -46.042 -27.979  22.385  1.00167.37           O
ATOM   6165  C3'  DA I -73     -45.006 -30.049  22.255  1.00166.94           C
ATOM   6166  O3'  DA I -73     -45.116 -31.421  22.619  1.00166.58           O
ATOM   6167  C2'  DA I -73     -45.629 -29.773  20.889  1.00167.20           C
ATOM   6168  C1'  DA I -73     -46.128 -28.331  21.012  1.00167.53           C
ATOM   6169   N9  DA I -73     -45.409 -27.347  20.184  1.00167.70           N
ATOM   6170   C8  DA I -73     -44.776 -26.213  20.626  1.00167.66           C
ATOM   6171   N7  DA I -73     -44.212 -25.500  19.679  1.00167.66           N
ATOM   6172   C5  DA I -73     -44.491 -26.208  18.522  1.00167.82           C
ATOM   6173   C6  DA I -73     -44.167 -25.976  17.163  1.00167.68           C
ATOM   6174   N6  DA I -73     -43.462 -24.917  16.750  1.00167.61           N
ATOM   6175   N1  DA I -73     -44.595 -26.874  16.245  1.00167.60           N
ATOM   6176   C2  DA I -73     -45.305 -27.933  16.662  1.00167.61           C
ATOM   6177   N3  DA I -73     -45.667 -28.258  17.908  1.00167.74           N
ATOM   6178   C4  DA I -73     -45.229 -27.349  18.808  1.00167.85           C
ATOM   6179    P  DT I -72     -43.906 -32.208  23.323  1.00166.33           P
ATOM   6180  OP1  DT I -72     -44.062 -32.031  24.784  1.00166.34           O
ATOM   6181  OP2  DT I -72     -42.638 -31.816  22.667  1.00166.28           O
ATOM   6182  O5'  DT I -72     -44.167 -33.748  22.962  1.00165.73           O
ATOM   6183  C5'  DT I -72     -45.409 -34.196  22.418  1.00164.98           C
ATOM   6184  C4'  DT I -72     -45.310 -34.425  20.919  1.00164.44           C
ATOM   6185  O4'  DT I -72     -45.104 -33.169  20.226  1.00164.50           O
ATOM   6186  C3'  DT I -72     -44.176 -35.341  20.471  1.00164.05           C
ATOM   6187  O3'  DT I -72     -44.756 -36.505  19.899  1.00163.49           O
ATOM   6188  C2'  DT I -72     -43.369 -34.526  19.455  1.00164.06           C
ATOM   6189  C1'  DT I -72     -44.333 -33.408  19.066  1.00164.11           C


Best,
Shuxiang

3
Web DSSR is a user-friendly web-based interface for analyzing and visualizing three-dimensional (3D) nucleic-acid-containing structures. The server allows the user to determine a wide variety of conformational parameters in a given PDB ID or uploaded structure. Meanwhile, the secondary structure visualization component offers simultaneously highlighting of 1D, 2D, and 3D nucleic-acid structures.

The wDSSR web server is located at http://web.x3dna-dssr.org/.

Any questions and bug reports are welcome!


4
Dear Xiangjun,

I used DSSR-enhanced visualization web server to display ribosome structures such as 5afi, 5j4b. All my tried failed. I'm not sure it is my browser problem or the web server inner error. Thank you.

Best,
Shuxiang   

5
Dear Xiangjun,

I tried to use the following dbn file generated by DSSR and display its RNA secondary structure in forna (a RNA secondary structure visualization tool). However, it looks like forna doesn't recognize multiple sequences and "&" notation. It there a way to get around this? Thank you.

>2F4V nts=1511 [2F4V] -- secondary structure derived by DSSR
UGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGG&CCGCGGGGUUUU&ACUCCG&UGGUC&AGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUU&GCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAA&CCCGGGACGAAACCCCCGACGA&GGGGACUGACGGUACCGGG&GUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCU&CCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGG&AGCCUACGGG&CAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUC&A&UUCU
....((((..[.[[[..)))).((((.(((((..(((((((((....(((.(((..(((..((.((&((((((((....&.)))))&)))))&.)))))......(((......((((((((..((...(((((((.(((((....((((((....)))))).....)))))....((((.(((((....))))).))))...((((...&)))).)))))))..))))))))))(((....(((..((((((((.......)))))))))))......)))..((((((((....))))...))))))).(((((............))))).((((....))))...)))))).).....(.(((...((.((....)).).))))).)).))))))..((((.......(((....)))......))))....&(.(((...(....((((.....&)))).....)....))).)&......((((([[[...(((((.....((.]]])).......))))))))))..)))))))))..........((([[...(.((((...(((.(((((((.((((((((((......((((((.....))))))....))))))))..)))))))))..(((.(((((...((((((((...(((((((....((........)).......)))))))...).......((....)).)))))))..)))))..))..))))...))))....((((((...((...((((.........))))...))))))))......{...((((((..((((((((((...&))))))))))...((..]])).....)))))))))).(((......((((....))))....)))...]]].](((((.(((((((.((..(((((..((((((((((......((........))..........((((((...(...((............(.(....).)........(((....).))........))).((.(((...((((((.(....(((((((((....)))..((((......))))..)))))).....((((.(((((.....(....(.......)..)......)))))..(..(((((....))))).....)..)))).....).).)))...)).))))).....))))))..[)).)))))))).(...(((((((.....(((..((..((((....))))..))....))).....)))))))......(....(((((((........)))))))....)..)..))))).....(((((((......]...)))))))......))...)))))))))).))..(.(..((.(.((((.(((..((.(((.((((((...(.((((...&.(((....))&).)))).)..)))))).))).))..))).))))..).))...)..)..(((((((((....)))))))))}....&.&....

Best,
Shuxiang                                                           


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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.