Haslina Asis

Assalam o alaikum wa rahmatullahi wa barkatuhu

Hope you doing well

First of all which format of the complex is used for analysis in ligplot? Secondly, you must check the server file and top-ranked complex selection, and ligplot only support pdb format.

@waseem

Hi, my complex has the lowest energy score and once downloaded from the server it is already in pdb format.

Thanks for your response.

Haslina Asis

LigPlot is designed for protein-ligand interaction visualization only (https://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/).

You can try PIMA server for visualization (http://caps.ncbs.res.in/pima/)

Regards

Jobin Thomas

Ligplot plus has option for protein-protein interaction using Dimplot option. however the file that I downloaded from Hdock cannot be viewed.

Thank you for your suggestion. Going to try for it.

To visualize a protein-protein docked complex in LigPlus, you need to first rename the chains of the proteins. As, initially, both chains are named 'Chain A', before visualization, you need to change the chain names. To rename the chains, PyMol can be used.