| Step |
Description |
View |
| 1 |
Click on Submit in the vertical menu on the left and then on Single PSN link on the right |
 |
| 2 |
- In this case example, the Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) (PDB: 1N77) will be used to build the PSG and to search for the shortest communication pathways.
The ATP molecule and all residues in the protein and the in tRNA will be included in the calculation
- Insert the PDB code 1N77 and then click Submit
|
 |
| 3 |
- Selection serves to indicate all residues (e.g. amino acids, nucleotides, small molecules, ions), which will be considered for building both the PSG and the shortest communication pathways. This example concerns a ternary complex involving tRNA, a protein (glutamyl-tRNA synthetase (GluRS), and ATP. The PDB contains two ternary complexes. Delete the asterisks in the B and D boxes to deselect all atoms from those chains so that only residues in chains C (tRNA) and A (GluRS and ATP) are included in calculations
- Click on Update View button to highlight selected atoms on the 3D viewer
|
 |
| 4 |
- Click on Unselect All button on the rightmost table to deselect all waters
- Click on Submit button above the table to submit the job
|
 |