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).

Example of pdb file format

[...]
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).

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
[...]
        

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).

Example of multimodel pdb file format

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).

Example of multimodel xyz file format

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
        

If empty - use first chain.

Starting index:
Ending index:

Define first and last index of atom/point for closing. If empty - use first and last point in chain.



KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling