Hi Arun thank you for your kind update and sure anytime:).

Please let me know where these missing residues are located i.e. are they in highly dynamic loop regions? are they located in parts of the protein that are pivotal towards ligand binding etc.? (These answers will allow me to guide you into the right direction.)

Best, Joel

On Fri, Sep 1, 2023 at 8:25 AM Arun Dhanasekaran via modeller_usage < modeller_usage@salilab.org> wrote:

> My reference pdb contains two chains of different protein, one with 306 > residues in which 39 residues are missing and another with 271 residues > with 22 residues are missing > > > > Thanks a lot for helping me …… > > > > Sent from Mail https://go.microsoft.com/fwlink/?LinkId=550986 for > Windows > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/ >

On 8/31/23 11:25 PM, Arun Dhanasekaran via modeller_usage wrote: > My reference pdb contains two chains of different protein, one with 306 > residues in which 39 residues are missing  and another with 271 residues > with 22 residues are missing

As others have said, adding missing residues for a multi-chain protein is exactly the same as for a single-chain protein, except that you need to add chain break characters ("/") between the chain sequences. Alternatively, add the missing residues for each chain individually and then combine the two models into one, e.g. with a package such as ChimeraX.

Ben Webb, Modeller Caretaker