if I understand you correctly, you are looking for a trimer (or hexamer ?) of heterodimers. Did you try to just 3D fit your monomer models against their counterpart in the yeast structure? How do this putative interfaces look like - do they appear to be conserved, or do you have any evidence that they are not, e.g. on the base of sequence conservation or surface hydrophobicity? You may have to prune back your alpha fold model to the regions predicted with a reasonably high confidence level, as alpha fold also gives you predictions for regions that may be natively unfolded, and these may clash in attempts to multimerize the structure.

You might try SymmDock http://bioinfo3d.cs.tau.ac.il/SymmDock/php.php to assemble the dimers into the hexamers.

If your template structure (from yeast) has the arrangement you want (a ring of heterodimers), then you can use the CIF file (obtained from Protein Data Bank) in alphafold to build the complex structure you want.

Annemarie Honegger Dear Dr. Honegger,

I was trying Symmdock. Previously it worked very well. Now when I am submitting my PDB file for job to run, it is giving a message like "You have uploaded an empty file: ClusPro81313910coot.pdb, size =". However, when I opening the same file in coot or pymol it is perfectly showing the structure. Any suggestions would be highly appreciated.

Thank you

With kind regards

Prem

What operating system are you working with? One possibility is that you have the wrong type of end-of-line characters. Make sure it uses the UNIX convention. It can also be some other subtle error in the file format, which most programs ignore, e.g. a single empty line where none is expected. It is hard to diagnose the problem without seeing the actual file that caused the problem.

Annemarie Honegger Thank you so much once again Dr. Honegger. There was "END" command missing in the PDB file. And I corrected it. Now the file is running on symmdock server. Thanks a lot for your help.

With humble regards

Prem