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).
[...]
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).
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:
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).
[...] 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).
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:
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