For more details on input and output information see:

For detailed information on the results see Interpreting knotting fingerprint.

Standard file format from pdb database. Server uses all ATOM and HETATM entries, and each of them is interpreted as a particle (or bead). Define chain index in submit form if your file contains more than one chain. By default, server uses the first chain. It is possible to send bzip2-compressed file (with extension *.pdb.bz2).

Example of pdb file format

[...]
HETATM 2564  N9  chr b 117      -2.915  -3.934  21.282  0.00  1.00           N   116800000
HETATM 2565  N10 chr b 117      -3.152  -3.819  20.587  0.00  1.00           N   116900000
HETATM 2566  N1  chr b 118      -3.069  -2.853  21.058  0.00  1.00           N   117000000
HETATM 2567  N2  chr b 118      -1.872  -2.504  20.513  0.00  1.00           N   117100000
HETATM 2568  N3  chr b 118      -1.244  -2.040  19.243  0.00  1.00           N   117200000
HETATM 2569  N4  chr b 118      -0.268  -1.462  19.127  0.00  1.00           N   117300000
HETATM 2570  N5  chr b 118      -0.655  -1.107  18.255  0.00  1.00           N   117400000
HETATM 2571  N6  chr b 118      -0.289  -0.796  18.384  0.00  1.00           N   117500000
HETATM 2572  N7  chr b 118      -0.059   0.283  18.731  0.00  1.00           N   117600000
HETATM 2573  N8  chr b 118       0.508   0.568  19.600  0.00  1.00           N   117700000
HETATM 2574  N9  chr b 118       1.123   0.855  18.530  0.00  1.00           N   117800000
HETATM 2575  N10 chr b 118       1.508   0.727  17.460  0.00  1.00           N   117900000
HETATM 2576  N1  chr b 119       0.279   0.575  17.550  0.00  1.00           N   118000000
HETATM 2577  N2  chr b 119      -0.344   1.101  17.402  0.00  1.00           N   118100000
HETATM 2578  N3  chr b 119      -0.837   1.240  17.916  0.00  1.00           N   118200000
HETATM 2579  N4  chr b 119      -1.557   1.203  17.170  0.00  1.00           N   118300000
HETATM 2580  N5  chr b 119      -2.218   0.503  16.737  0.00  1.00           N   118400000
HETATM 2581  N6  chr b 119      -3.190   0.969  17.021  0.00  1.00           N   118500000
[...]
        

A simple format which only contains atom numbers along the chain (in the first column) and Cartesian coordinates of all atoms in a chain (in second, third and fourth column); such a file cannot contain any additional columns. This format is suitable for analysis of chains other than proteins. It is possible to send bzip2-compressed file (with extension *.xyz.bz2).

Example of xyz file format

1       65.749        -49.197          15.303
2       69.453        -49.413          16.193
3       71.017        -51.127          19.196
4       72.074        -54.316          20.982
5       70.209        -57.190          22.570
6       70.849        -60.560          24.165
7       69.045        -63.421          22.445
8       68.973        -66.376          24.884
9       67.367        -68.701          22.324
[...]
        

In N3D format, a single chain (chromosome) begins with a header containing: a name of the chromosome, number of beads in the chain and a number of models for a given chain. Each particle entry contains number of a bead or other measure of chain extension, followed by groups of three numbers representing cartesian coordinates for each model (number of coordinates groups is equal to the number of declared models in the header).

Important:

  • Note 1: Chromosome chain name must start with a letter.
  • Note 2: Beacause of the server requirements, we rename chain names with single characters, in the following order: a-z0-9A-Z.
  • Note 3: If the maximal value in the first column (bead number) is larger than 99999, then these numbers are renumbered into 1,2,3…

Example of n3d file format

chrA    9       1
1       65.749        -49.197          15.303
2       69.453        -49.413          16.193
3       71.017        -51.127          19.196
4       72.074        -54.316          20.982
5       70.209        -57.190          22.570
6       70.849        -60.560          24.165
7       69.045        -63.421          22.445
8       68.973        -66.376          24.884
9       67.367        -68.701          22.324
        

Standard file format from pdb database. Server uses all ATOM and HETATM entries, and each of them is interpreted as a particle (or bead). Chromosomes are distinguished by the chain name entry. It is possible to send bzip2-compressed file (must have *.pdb.bz2).

Example of multimodel pdb file format

[...]
HETATM 2564  N9  chr b 117      -2.915  -3.934  21.282  0.00  1.00           N   116800000
HETATM 2565  N10 chr b 117      -3.152  -3.819  20.587  0.00  1.00           N   116900000
HETATM 2566  N1  chr b 118      -3.069  -2.853  21.058  0.00  1.00           N   117000000
HETATM 2567  N2  chr b 118      -1.872  -2.504  20.513  0.00  1.00           N   117100000
HETATM 2568  N3  chr b 118      -1.244  -2.040  19.243  0.00  1.00           N   117200000
HETATM 2569  N4  chr b 118      -0.268  -1.462  19.127  0.00  1.00           N   117300000
HETATM 2570  N5  chr b 118      -0.655  -1.107  18.255  0.00  1.00           N   117400000
HETATM 2571  N6  chr b 118      -0.289  -0.796  18.384  0.00  1.00           N   117500000
HETATM 2572  N7  chr b 118      -0.059   0.283  18.731  0.00  1.00           N   117600000
HETATM 2573  N8  chr b 118       0.508   0.568  19.600  0.00  1.00           N   117700000
HETATM 2574  N9  chr b 118       1.123   0.855  18.530  0.00  1.00           N   117800000
[...]
HETATM 9464  N8  chr g  22       5.441   0.894  -0.097  0.00  1.00           N    21700000
HETATM 9465  N9  chr g  22       6.087  -0.114   1.467  0.00  1.00           N    21800000
HETATM 9466  N10 chr g  22       4.999   0.201   1.999  0.00  1.00           N    21900000
HETATM 9467  N1  chr g  23       5.072  -0.605   1.072  0.00  1.00           N    22000000
HETATM 9468  N2  chr g  23       4.649  -0.256  -0.038  0.00  1.00           N    22100000
HETATM 9469  N3  chr g  23       4.212   0.527  -0.863  0.00  1.00           N    22200000
HETATM 9470  N4  chr g  23       4.329   0.676  -1.936  0.00  1.00           N    22300000
HETATM 9471  N5  chr g  23       5.090   1.555  -2.078  0.00  1.00           N    22400000
HETATM 9472  N6  chr g  23       4.893   2.254  -2.264  0.00  1.00           N    22500000
HETATM 9473  N7  chr g  23       3.887   1.883  -2.766  0.00  1.00           N    22600000
HETATM 9474  N8  chr g  23       2.949   2.231  -3.080  0.00  1.00           N    22700000
HETATM 9475  N9  chr g  23       2.050   2.167  -3.600  0.00  1.00           N    22800000
[...]

xyz format (which only contains atom numbers along the chain and Cartesian coordinates of all atoms in a chain), in which consecutive chromosome chains are separated by "CHN" header followed by a letter specifying chromosome. The last line of the file must contain "END". It is possible to send bzip2-compressed file (with extension *.xyz.bz2).

Example of multimodel xyz file format

CHN a
1 309.520 300.740 308.220
2 307.970 302.000 304.930
3 309.710 303.310 301.740
4 311.370 299.900 301.510
[...]
81 288.870 295.970 282.810
82 288.490 293.410 280.000
CHN b
1 311.350 305.300 304.570
2 309.880 304.440 301.160
3 310.700 304.940 297.380
4 312.410 301.520 297.640
[...]
81 298.250 283.500 285.870
82 296.820 280.060 286.010
END
        

In N3D format, a file containing multiple chains is formed from single chains entries.

Please remember that:

  • Note 1: Chromosome chain name must start with a letter.
  • Note 2: Beacause of the server requirements, we rename chain names with single characters, in the following order: a-z0-9A-Z.
  • Note 3: If the maximal value in the first column (bead number) is larger than 99999, then these numbers are renumbered into 1,2,3…

Example of multichain n3d file format

chrA    9       1
1       65.749        -49.197          15.303
2       69.453        -49.413          16.193
3       71.017        -51.127          19.196
4       72.074        -54.316          20.982
5       70.209        -57.190          22.570
6       70.849        -60.560          24.165
7       69.045        -63.421          22.445
8       68.973        -66.376          24.884
9       67.367        -68.701          22.324
chrB    9       1
1       65.749        -49.197          15.303
2       69.453        -49.413          16.193
3       71.017        -51.127          19.196
4       72.074        -54.316          20.982
5       70.209        -57.190          22.570
6       70.849        -60.560          24.165
7       69.045        -63.421          22.445
8       68.973        -66.376          24.884
9       67.367        -68.701          22.324
        

If empty - use first chain.

If empty - use first chromosome block.

If empty - use first model.

Random closure number of tries. Default: 10

Matrix resolution:

Default: 7

Knot strength threshold for matrix resolution (in %):

Default: 20

Thresholds for complex structures (in %)

Default: 40.

Default: 30.




KnotGenom | Interdisciplinary Laboratory of Biological Systems Modelling