i am trying to do comparative homology modeling of a dimer. does the input pdb have to have the dimer with both monomer threaded?
when i input a dimer pdb with grishin alignment file of the monomer i get a threaded pdb with only the monomer. can i use this pdb as the input pdb or do i need to thread the other monomer and add that to the input pdb? thanks!
oh and by the way is the robetta server down? thanks.
You certainly should be able to do RosettaCM with symmetric proteins: See https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM#running-the-rosettacm-protocol_other-tips for more information. Once you've made the changes, you would thread the asymmetric unit onto the templates, and RosettaCM will automatically generate the symmetry related versions.
Also, it looks like Robetta is back up.