lightdock pdb file visualises incorrectly in pymol

[lightdock]

lightdock pdb file visualises incorrectly in pymol

[JorgeRoel]

My bet is on 1), both have chainID A (they look like AlphaFold predictions)

[alchemistcai]

I used to meet similar problem.The proteins may have same chain names,say chain A,which confuses pymol the connection table of proteins.Use pymol's alter chain A,chain='B' command to alter one of the chain name.

That's why in official tutorials,the receptor's chain is R and the ligand's chain is L.

[alchemistcai]

Or alter resi =int(resi)+1000 of one protein to avoid residues numbers conflict before setup and docking.

[Jorisvansteenbrugge]

@brianjimenez Thanks for the reply. It was indeed option 1), like @JorgeRoel and @alchemistcai mentioned. After renaming the chains everything worked as expected. Thank you.

[brianjimenez]

This is probably caused by 1) same chains on receptor and ligand or 2) no chain Ids assigned in the input PDB structures. Please note this is a problem with PyMol software, if you open the predicted structures with a different software (ChimeraX, etc.) you won't probably experience this issue. Please, could you check @Jorisvansteenbrugge ?