I think the only trick is not forgetting the chain break in the ali file: https://salilab.org/modeller/manual/node29.html
Best, Ajasja
PS: It's a very broad question, so I can only give a broad reply.
On Thu, 31 Aug 2023 at 09:12, Arun Dhanasekaran via modeller_usage < modeller_usage@salilab.org> wrote:
> i tried a build a homology model of a heterodimer protein,since it > contains missing residue i have to model that. But i am only familiar > with single chain homology modelling and fro multi chain i am getting many > errors like in greeting ali flie. and from tutorial also i am not getting > everything clearly. can i get a detailed explantiojn on multi chain > modelling > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/