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/