You can use discovery studio visualizer for that

Use the Protein-Ligand Interaction Profiler PLIP https://projects.biotec.tu-dresden.de/plip-web/plip (Webserver, application also available for download) - it will not only catalog the different types of interactions, but also produce a PyMOL .pse file visualizing the different interactions.

Annemarie Honegger

i tried to use online PLIP but it didnt show all types of interaction.

What type of interactions are you missing - did you check under "HELP" whether that type is generally not in the list of recognized interaction, or whether in your case the interaction is just outside the tolerance for recognition? Be aware that for water-bridged interactions, the water molecules involved need to be present in your input file. You can always post-process the .pse generated by PLIP in PyMOL.

im looking for the hydrophobic / pi - pi stacking interaction and the metal co-ordination bonds.

can i view these type from the HELP ?

The Help page (https://projects.biotec.tu-dresden.de/plip-web/plip/help) shows you examples of how the different interactions are represented in the output files, and if you scroll down to the bottom, you get a list of the cut-off distances beyond which the interaction is no longer considered to be there.

Hydrophobic interactions should show up as gray dashed lines, Pi-interactions as dashed lines from small spheres indicating the center of the ring systems, metal complexes as purple dashed lines from the metal ion to coordinating protein groups. As these are also listed as objects in the .pse file, you can change the representation to fit your style.

If the interactions you expect are not found, you should have to check the input file carefully - are the distances too large? Do you get any error message. If you send me a sample pdb file, I'll have a look at it.

Thank you very much Annemarie. i will try to do the tips you told me and if i couldnt make it i will send it to you