Look at the Protein-Ligand Interaction Profiler (PLIP), available as Server or stand-alone application. https://projects.biotec.tu-dresden.de/plip-web/plip/
It does a nice job at cataloging and visualization of Protein-Ligand interactions and produces PyMOL .pse files of the results.
Visualization of Protein-Ligand interactions using PyMOL is one of the best interface.
I have used PyMOL Which shows only H-bonding as dotted lines.Other bonding like pi-pi & hydrophobic bonding are not visible.Moreover, in docking studies of my compound it shows something interesting! I wanted to know Which type of bonding it is (Dotted balls)? or it is something else.
I have used PyMOL Which shows only H-bonding as dotted lines.Other bonding like pi-pi & hydrophobic bonding are not visible.Moreover, in docking studies of my compound it shows something interesting! I wanted to know Which type of bonding it is (Dotted balls)? or it is something else.
Look at PLIP (https://projects.biotec.tu-dresden.de/plip-web/plip/). It produces a PyMOL file with differentiated representations of different interactions. See http://plip.biotec.tu-dresden.de/plip-web/plip/help on how it represents things like hydrophobic interactions, pi-pi stacking, cation-pi interactions, salt bridges, metal complexes, salt bridges and so on. You can then look at the output file in PyMOL and selectively switch on and off the display of the different interactions, as they are given as named selections, can change the color and so on.
"I wanted to know Which type of bonding it is (Dotted balls)? or it is something else". Do you mean the gray balls? These seem to be unconnected atoms - click on them to get their ID! (and make sure the molecules you docked have correct bond lengths by minimizing them in an appropriate program before docking)... or the yellow dotted lines? These seem to be hydrogen bonds - display the hydrogens to see if this is the case.
Use Discovery Studio. Both 2D and 3D interaction could achieved with good quality of all bond interaction.
Yes, Discovery studio would help you further dotted interaction.
Hi, for this end you can save the best pose and import it in to a pose viewer like ligplot, pymol and MOE