Using the command "alphafold predict #1,2" is handing the 3 monomer sequences (two from the #1 dimer, and one from the #2 monomer) to Alphafold and making a prediction for the interaction of those 3 monomers.  It is not using the PDB models of the dimer and monomer.  AlphaFold does not dock existing models, it makes predictions from sequences.

Tom


On Oct 5, 2022, at 6:44 AM, Tan, Wei Ren via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hence, how can I load the pdb of 6z1n (the heterodimer) and the sequence of the protein of interest to predict what is the possible interaction between the 2, instead of putting all 3 monomers as a sequence and for Alphafold to repredict the interactions between the2 monomers within 6z1n instead?