SASREF/Crysol CORAL DNA atoms not recognized

Global minimization programs: SASREF, CORAL, BUNCH, GLOBSYMM
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mawhite
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SASREF/Crysol CORAL DNA atoms not recognized

#1 Post by mawhite » 2021.04.24 03:39

Hello,

I am seeing a common problem with the recognition of DNA atoms in several packages (ATSAS3.03)

Three letter DNA residue names are not recognized at all.

The atoms OP1, OP2, O1P, O2P are never recognized whether using single or double letter residue names ( G, C, A, T or DG, DC, DA, DT)

Whether using ( DG, DC, DA, DT) or ( G, C, A, T) residue names the atoms C1',C2',C3',C4',C5',O3' O5', O6, OP1, OP2, O1P, O2P are not recognized.
or if using * for prime atoms O5*, C7, O6, OP1, OP2, O1P, O2P are not recognized.
Processing atoms :Warning: unknown residue / atom ID in line ATOM 3 O5* C M 1
Warning: unknown residue / atom ID in line ATOM 18 OP1 C M 1
Warning: unknown residue / atom ID in line ATOM 19 OP2 C M 1
Warning: unknown residue / atom ID in line ATOM 22 O5* T M 2
Warning: unknown residue / atom ID in line ATOM 37 C7 T M 2
Warning: unknown residue / atom ID in line ATOM 38 OP1 T M 2
Warning: unknown residue / atom ID in line ATOM 39 OP2 T M 2
...
Warning: unknown residue / atom ID in line ATOM 287 O5* A M 15
Warning: unknown residue / atom ID in line ATOM 304 OP1 A M 15
Warning: unknown residue / atom ID in line ATOM 305 OP2 A M 15
Warning: unknown residue / atom ID in line ATOM 322 O6 G M 16
Warning: unknown residue / atom ID in line ATOM 326 OP1 G M 16
Warning: unknown residue / atom ID in line ATOM 327 OP2 G M 16
The PDB file has these entries:

Code: Select all

ATOM      1  P    DC M   1      -2.794  49.636   4.288  1.00 20.00           P  
ATOM      2  C5*  DC M   1      -0.816  50.368   2.701  1.00 20.00           C  
ATOM      3  O5*  DC M   1      -1.468  50.464   3.981  1.00 20.00           O  
ATOM      4  C4*  DC M   1      -0.420  51.743   2.217  1.00 20.00           C  
ATOM      5  O4*  DC M   1      -1.610  52.517   1.949  1.00 20.00           O  
ATOM      6  C3*  DC M   1       0.369  52.566   3.229  1.00 20.00           C  
ATOM      7  O3*  DC M   1       1.776  52.348   3.085  1.00 20.00           O  
ATOM      8  C2*  DC M   1       0.011  53.993   2.860  1.00 20.00           C  
ATOM      9  C1*  DC M   1      -1.400  53.884   2.289  1.00 20.00           C  
ATOM     10  N1   DC M   1      -2.466  54.288   3.219  1.00 20.00           N  
ATOM     11  C2   DC M   1      -2.637  55.646   3.505  1.00 20.00           C  
ATOM     12  O2   DC M   1      -1.886  56.473   2.966  1.00 20.00           O  
ATOM     13  N3   DC M   1      -3.617  56.023   4.358  1.00 20.00           N  
ATOM     14  C4   DC M   1      -4.407  55.103   4.915  1.00 20.00           C  
ATOM     15  N4   DC M   1      -5.359  55.521   5.751  1.00 20.00           N  
ATOM     16  C5   DC M   1      -4.255  53.713   4.640  1.00 20.00           C  
ATOM     17  C6   DC M   1      -3.284  53.354   3.792  1.00 20.00           C  
ATOM     18  OP1  DC M   1      -3.209  49.944   5.680  1.00 20.00           O  
ATOM     19  OP2  DC M   1      -3.747  49.866   3.172  1.00 20.00           O1-
ATOM     20  P    DT M   2       2.683  52.136   4.384  1.00 20.00           P  
ATOM     21  C5*  DT M   2       3.703  54.423   3.545  1.00 20.00           C  
ATOM     22  O5*  DT M   2       3.289  53.586   4.642  1.00 20.00           O  
ATOM     23  C4*  DT M   2       3.619  55.882   3.933  1.00 20.00           C  
ATOM     24  O4*  DT M   2       2.243  56.234   4.213  1.00 20.00           O  
ATOM     25  C3*  DT M   2       4.425  56.263   5.177  1.00 20.00           C  
ATOM     26  O3*  DT M   2       5.182  57.452   4.929  1.00 20.00           O  
ATOM     27  C2*  DT M   2       3.369  56.499   6.243  1.00 20.00           C  
ATOM     28  C1*  DT M   2       2.164  56.941   5.438  1.00 20.00           C  
ATOM     29  N1   DT M   2       0.874  56.611   6.068  1.00 20.00           N  
ATOM     30  C2   DT M   2       0.074  57.646   6.494  1.00 20.00           C  
ATOM     31  O2   DT M   2       0.380  58.820   6.369  1.00 20.00           O  
ATOM     32  N3   DT M   2      -1.108  57.253   7.071  1.00 20.00           N  
ATOM     33  C4   DT M   2      -1.555  55.960   7.264  1.00 20.00           C  
ATOM     34  O4   DT M   2      -2.641  55.761   7.800  1.00 20.00           O  
ATOM     35  C5   DT M   2      -0.663  54.925   6.795  1.00 20.00           C  
ATOM     36  C6   DT M   2       0.493  55.298   6.230  1.00 20.00           C  
ATOM     37  C7   DT M   2      -1.062  53.493   6.961  1.00 20.00           C  
ATOM     38  OP1  DT M   2       3.794  51.219   4.024  1.00 20.00           O  
ATOM     39  OP2  DT M   2       1.786  51.796   5.517  1.00 20.00           O1-
...
ATOM    285  P    DA M  15      -9.384  64.533  12.916  1.00 20.00           P  
ATOM    286  C5*  DA M  15      -7.050  65.476  12.121  1.00 20.00           C  
ATOM    287  O5*  DA M  15      -8.266  64.771  11.807  1.00 20.00           O  
ATOM    288  C4*  DA M  15      -6.000  65.203  11.070  1.00 20.00           C  
ATOM    289  O4*  DA M  15      -5.626  63.811  11.104  1.00 20.00           O  
ATOM    290  C3*  DA M  15      -6.444  65.480   9.633  1.00 20.00           C  
ATOM    291  O3*  DA M  15      -5.869  66.701   9.154  1.00 20.00           O  
ATOM    292  C2*  DA M  15      -5.885  64.314   8.830  1.00 20.00           C  
ATOM    293  C1*  DA M  15      -5.123  63.461   9.831  1.00 20.00           C  
ATOM    294  N1   DA M  15      -2.983  59.029   8.355  1.00 20.00           N  
ATOM    295  C2   DA M  15      -2.509  60.279   8.420  1.00 20.00           C  
ATOM    296  N3   DA M  15      -3.121  61.393   8.818  1.00 20.00           N  
ATOM    297  C4   DA M  15      -4.388  61.132   9.182  1.00 20.00           C  
ATOM    298  C5   DA M  15      -5.019  59.902   9.166  1.00 20.00           C  
ATOM    299  C6   DA M  15      -4.261  58.802   8.728  1.00 20.00           C  
ATOM    300  N6   DA M  15      -4.736  57.557   8.658  1.00 20.00           N  
ATOM    301  N7   DA M  15      -6.328  60.016   9.610  1.00 20.00           N  
ATOM    302  C8   DA M  15      -6.459  61.292   9.878  1.00 20.00           C  
ATOM    303  N9   DA M  15      -5.321  62.025   9.649  1.00 20.00           N  
ATOM    304  OP1  DA M  15      -9.789  65.858  13.449  1.00 20.00           O  
ATOM    305  OP2  DA M  15     -10.415  63.615  12.368  1.00 20.00           O1-
ATOM    306  P    DG M  16      -6.402  67.361   7.793  1.00 20.00           P  
ATOM    307  C5*  DG M  16      -4.005  66.974   6.750  1.00 20.00           C  
ATOM    308  O5*  DG M  16      -5.428  66.756   6.686  1.00 20.00           O  
ATOM    309  C4*  DG M  16      -3.283  66.022   5.825  1.00 20.00           C  
ATOM    310  O4*  DG M  16      -3.503  64.656   6.243  1.00 20.00           O  
ATOM    311  C3*  DG M  16      -3.705  66.097   4.352  1.00 20.00           C  
ATOM    312  O3*  DG M  16      -2.566  66.372   3.523  1.00 20.00           O  
ATOM    313  C2*  DG M  16      -4.204  64.700   4.031  1.00 20.00           C  
ATOM    314  C1*  DG M  16      -3.543  63.844   5.089  1.00 20.00           C  
ATOM    315  N1   DG M  16      -3.584  58.778   4.935  1.00 20.00           N  
ATOM    316  C2   DG M  16      -2.613  59.654   4.519  1.00 20.00           C  
ATOM    317  N2   DG M  16      -1.512  59.106   3.986  1.00 20.00           N  
ATOM    318  N3   DG M  16      -2.717  60.969   4.613  1.00 20.00           N  
ATOM    319  C4   DG M  16      -3.888  61.344   5.169  1.00 20.00           C  
ATOM    320  C5   DG M  16      -4.921  60.549   5.619  1.00 20.00           C  
ATOM    321  C6   DG M  16      -4.800  59.141   5.505  1.00 20.00           C  
ATOM    322  O6   DG M  16      -5.606  58.266   5.846  1.00 20.00           O  
ATOM    323  N7   DG M  16      -5.957  61.325   6.120  1.00 20.00           N  
ATOM    324  C8   DG M  16      -5.543  62.553   5.970  1.00 20.00           C  
ATOM    325  N9   DG M  16      -4.290  62.635   5.412  1.00 20.00           N  
ATOM    326  OP1  DG M  16      -6.163  68.824   7.869  1.00 20.00           O  
ATOM    327  OP2  DG M  16      -7.775  66.853   7.543  1.00 20.00           O1-
I am worried that these atoms and residues may be excluded from any calculations and will bias the results.

Is this a problem with the ATOM format or names with the ATSAS programs?

Does this warning affect the Calculation of scattering in Crysol or CORAL?

Best regards
Mark
Last edited by mawhite on 2021.05.24 20:16, edited 1 time in total.

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AL
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Example files

#2 Post by AL » 2021.05.17 15:58

Thank you for reporting this.
Could you please attach some examples?

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Re: Example files

#3 Post by AL » 2021.05.27 16:06

Thank you for providing an example, we will investigate this.

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Re: SASREF/Crysol CORAL DNA atoms not recognized

#4 Post by AL » 2021.05.28 10:37

Apparently, the DC nucleotide does not have an atom C5*, it should be C5'.
C5* seems to be an older naming convention. You may try using CRYSOL with the -old option, it will resolve some but not all of the warnings. We recommend using PDB files in the latest format.

mawhite wrote:
2021.04.24 03:39
I am worried that these atoms and residues may be excluded from any calculations and will bias the results.
...
Does this warning affect the Calculation of scattering in Crysol or CORAL?
CRYSOL will treat all unknown atoms as oxygens.

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