Step	Action
Note 1	Modelling of oligomeric proteins with SwissModel can only be done in Optimize (Project) Mode. The Combine Mode of version 3.0 is no longer supported.
Note 2	Please use the latest version of SwissPDB-Viewer, which you can download from this server.
1	Identify the correct template for your sequence. (The PQS server at EBI may give you more information about the olimeric state of your template.) Make sure, your protein really has the same quaternary structure as the template!
2	Identify the correct protomer template for each chain to be modelled. (See PQS and the REAMRK 350 lines in the template PDB-file to construct the correct protein quaternary structure.) Build a seperate model for each chain based on the identified protomer template.
3	If you succeeded in Step 2: Use SPDBV to construct a quaternary structure template following these rules: Use different chain-names for each protomer template (e.g. A,B,C ...). Merge all protomer templates in one layer. Make sure, the template contain NO heteroatoms or modifies residues. Save the quaternary structure template to disk.
4	Check your quaternary structure template visually (color by chain may help.) Each chain has a unique chain name? All protein-protein contact surfaces are correct? No collisions? No isolated protomers?
5	Use a text editor to prepare a sequence file in FASTA format containing the sequences to be modelled (in the same order as the protomer templates), seperated by semicolons ";" like this: >ModelName MONOMERASEQUENCE;MONOMERBSEQUENCE
6	Load your quaternary structure template and the FASTA sequence into SPDBV. Fit the sequence to the template. Use the align window to adjust the alignment manually if needed.
7	Submit your request to SwissModel. Good luck with your project!