Author Topic: strange residue number after dssr --view option (Read 51410 times)

shuxiang · « **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

xiangjun · « **Reply #1 on:** August 06, 2018, 05:26:49 pm »

Hi Shuxiang,

You've touched a subtle point in the labeling of residues (nucleotides) in mmCIF vs. PDB. Using PDB entry 3mgp, as you used, as an example, an excerpt for the corresponding PDB and mmCIF files (all downloaded from RCSB PDB) for I.DA.-73 is as below:

# PDB format
ATOM   6169  O5'  DA I -73       2.638   0.163  93.308  1.00166.52           O  
ATOM   6170  C5'  DA I -73       3.279   0.178  94.579  1.00166.78           C  
ATOM   6171  C4'  DA I -73       3.645  -1.223  95.042  1.00167.01           C  
ATOM   6172  O4'  DA I -73       2.489  -2.096  95.012  1.00167.37           O  
ATOM   6173  C3'  DA I -73       4.650  -1.969  94.180  1.00166.94           C  
ATOM   6174  O3'  DA I -73       5.972  -1.523  94.462  1.00166.58           O  
ATOM   6175  C2'  DA I -73       4.428  -3.410  94.635  1.00167.20           C  
ATOM   6176  C1'  DA I -73       2.941  -3.442  94.998  1.00167.53           C  
ATOM   6177  N9   DA I -73       2.097  -4.257  94.106  1.00167.70           N  
ATOM   6178  C8   DA I -73       0.995  -3.832  93.410  1.00167.66           C  

#mmCIF:
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

As noted in the mmCIF header, the sequence number "-73" matches "_atom_site.auth_seq_id", and number "1" matches "_atom_site.label_seq_id". Since the corresponding PDB entry uses _atom_site.auth_seq_id (-73), DSSR follows that convention.

DSSR currently has no option to employ the labeling "_atom_site.label_seq_id" while "_atom_site.auth_seq_id" exists.

Best regards,

Xiang-Jun

shuxiang · « **Reply #2 on:** August 06, 2018, 05:40:26 pm »

Hi Xiang-Jun,

Thank you very much for your explanation. I will fix the server to correctly represent these structures (such as 3mgp) with conflicts between "_atom_site.label_seq_id" and "_atom_site.auth_seq_id".

Best

,
Shuxiang

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Author Topic: strange residue number after dssr --view option (Read 51410 times)

shuxiang

strange residue number after dssr --view option

xiangjun

Re: strange residue number after dssr --view option

shuxiang

Re: strange residue number after dssr --view option