For more details on input and output information see:
For detailed information on the resulting plots and topological fingerprint see Interpret knotting data.Standard file format from pdb database. Server uses only Cα atoms. 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).
[...]
ATOM 24 CA GLU A 24 14.212 33.180 1.863 1.00 64.63 C
ATOM 25 CA GLU A 25 16.086 31.678 -1.097 1.00 59.03 C
ATOM 26 CA GLU A 26 15.156 34.903 -2.877 1.00 41.85 C
ATOM 27 CA GLY A 27 17.541 36.952 -0.744 1.00 46.12 C
ATOM 28 CA VAL A 28 15.113 37.849 2.017 1.00 38.98 C
ATOM 29 CA GLU A 29 16.989 38.371 5.242 1.00 43.20 C
ATOM 30 CA TRP A 30 15.083 39.568 8.265 1.00 23.42 C
ATOM 31 CA GLY A 31 16.419 41.023 11.489 1.00 19.92 C
ATOM 32 CA TYR A 32 16.084 43.613 14.220 1.00 20.17 C
ATOM 33 CA GLU A 33 18.064 46.492 12.735 1.00 20.57 C
[...]
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).
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 only Cα atoms (we recommends to grep-out other atoms to get smaller file). It is possible to send bzip2-compressed file (must have *.pdb.bz2).
MODEL 1 ATOM 1 CA LEU A 1 -2.440 -1.220 15.860 1.00 0.00 C ATOM 2 CA VAL A 2 -5.490 0.610 15.860 1.00 0.00 C ATOM 3 CA PHE A 3 -4.880 3.050 12.810 1.00 0.00 C ATOM 4 CA GLY A 4 -3.660 -0.610 10.980 1.00 0.00 C ATOM 5 CA ALA A 5 -6.710 -1.830 11.590 1.00 0.00 C ATOM 6 CA TRP A 6 -8.540 1.830 10.370 1.00 0.00 C ATOM 7 CA ALA A 7 -6.100 1.830 7.320 1.00 0.00 C ENDMDL MODEL 2 ATOM 1 CA LEU A 1 -2.440 -1.220 15.860 1.00 0.00 C ATOM 2 CA VAL A 2 -6.100 0.610 15.860 1.00 0.00 C ATOM 3 CA PHE A 3 -4.880 2.440 12.810 1.00 0.00 C ATOM 4 CA GLY A 4 -3.660 -1.220 10.980 1.00 0.00 C ATOM 5 CA ALA A 5 -7.320 -1.830 11.590 1.00 0.00 C ATOM 6 CA TRP A 6 -8.540 1.220 10.370 1.00 0.00 C ATOM 7 CA ALA A 7 -6.100 1.220 7.320 1.00 0.00 C ENDMDL
Typical output format from Gromacs package. It must be uploaded together with *.gro/*.pdb file to uncompress correctly.
xyz format (which only contains atom numbers along the chain and Cartesian coordinates of all atoms in a chain), in which consecutive time frames are separated by letter "t" followed by a number specifying moment of time. It is possible to send bzip2-compressed file (with extension *.xyz.bz2).
t 0.00000
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
t 1.25000
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