The comparison application is designed to help users look at the structural variations in a collection of NMR models or between two X-ray crystallography structures.
To analyse a NMR structures all you have to do is upload a single PDB using the file uploader in protein box #1. You can ignore the Chain & Alternative Name boxes as they are irrelevant. In the Start and End boxes you must insert the start position and end position of the fragment that you want to examine. Both values must be in the column marked with the *. For example you could use a start point of 2 and an end point of 9 if you only had the following PDB data.
* ATOM 2 CA ALA A 2 39.866 21.059 8.959 1.00 29.93 C ATOM 7 CA ASP A 3 43.425 19.735 8.836 1.00 26.30 C ATOM 15 CA LYS A 4 44.119 17.105 6.147 1.00 21.23 C ATOM 24 CA GLU A 5 45.918 15.101 8.820 1.00 16.83 C ATOM 33 CA LEU A 6 42.800 14.764 10.998 1.00 13.31 C ATOM 41 CA LYS A 7 42.788 11.087 12.105 1.00 12.56 C ATOM 50 CA PHE A 8 39.620 9.225 11.057 1.00 9.01 C ATOM 61 CA LEU A 9 38.249 5.964 12.522 1.00 7.65 C ATOM 69 CA VAL A 10 36.051 4.078 9.925 1.00 6.86 COnce complete, select the 'Is it NMR?' toggle and click 'Process Us'. The result will be an alignment of the fragments from each of the models in the NMR file. You can choose which methods to use (currently DSSP & Stride only) and the type of output (reduced three state** or original output).
To examine X-ray structures two files must be uploaded. For each of the proteins a chain, start and end point must be defined. The difference between the start and end point must be the same for each of the proteins, this allows you to compare different fragments from each protein. For example you could compare positions 2:20 of 3CHY chain A to 22:40 of 1HNN chain A (although that wouldn't make much sense). Because you are looking at X-ray structures you should pass the NMR toggle and go straight to 'Process Us'.
This part of the site requires that structures are uploaded to our server, to avoid name clashes a random name is assigned to your structure. If you wish to name your proteins once they are uploaded you can define an alternative name, otherwise the protein in the first box will be assigned the label (A) and the protein in the second box will be identified by (B).
There are a couple of variations on the reduced three state model, on this site Three State works as follows: