Problem with ligand-RMSD (l-RMSD) calculation in the basic protein-protein docking tutorial

I am working through the basic HADDOCK2.4 tutorials and have encountered an issue with one of the suggested command lines for PyMOL.

When I enter this command into PyMOL, I get the following error message:

ExecutiveRMS-Error: No atoms selected.

I am very new to this, so suspect there is an easy solution to this issue. I would really appreciate some advice. Thanks in advance!

This error is somewhat related to the command you inputted in PyMol, maybe you missed some - there’s no way to tell from your post.

I’d suggest you go traceback and re-do the pymol commands! good luck! :four_leaf_clover:


Thank you for your response. I have tried going back and repeating exactly as described in the tutorial but have had no success and get the same error each time. I have since tried the same command with my own docking run to get a CAPRI score for the clusters generated, but am met with the same error again.

I am a complete beginner with docking and coding, so unfortunately cannot see any way to troubleshoot by myself, since the script I have entered is - as far as I can tell - identical to the one given in the tutorial.

Which version of pymol are you using?

Again the commands are working - I gave yesterday this tutorial in the bioexcel online course…