I ran a successful docking of my proteins (antibody and antigen). However, for RMSD calculation in PYMOL, I need a merged file of two PDB structures. What is the best way to create a matching file that can be used to calculate the RMSD value with the docked cluster file?
I ran a successful docking of my proteins (antibody and antigen). However, for RMSD calculation in PYMOL, I need a merged file of two PDB structures. What is the best way to create a matching file that can be used to calculate the RMSD value with the docked cluster file?
What do you mean by a merged file?
The HADDOCK models contain the full complex.
Or do you refer to a known complex to which you want to compare by calculating RMSDs?
Check also our antibody-antigen docking tutorial:
https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-antibody-antigen/