I have docked 2 ligand simultaneously and tried to get 2d interactions with ligplot+ but in ligplot+ it is showing only one ligand ?

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Lakshmanan Loganathan

If your complex molecule has multiple ligands, Yes you can able to select the ligand in the view option.

Please refer to section 3 in the below link.

https://www.ebi.ac.uk/thornton-srv/software/LigPlus/manual/manual.html

Ashutosh Pal

Thank you for your help but what if file consider 2 ligand as 1 so is there any way to separate them