C-termini remodelling of dimeric structure removes second chain

[Anonymous]

Dear Rosetta Community,

I am trying to remodel a short C-terminal loop into  a docked dimeric structure consisting of 2 identical proteins and while the modeling itself worked, the output contains only the first protein.  The flags I used are the following:

-in:file:s bestp1.pdb

-remodel:blueprint c-term.remodel

-no_optH false

-ex1

-ex2

-remodel:num_trajectory 1

-remodel:quick_and_dirty

-out:file:scorefile miss_cterm.sc

( blueprint and pdb file are attached )

Unfortunatly the missing loop resides in the binding cleft between the proteins so that adding the second protein after remodeling results in clashes as the loop overlapps with residues from the second protein. So just model the first protein alone and then merge them is not an option for me. 

I have tried multiple things including merging the dimer, removing the chain identifiers (as hinted in: https://www.rosettacommons.org/node/10708 )  and switching the chains, but none of it worked.

Strangely enough doing the same procedure with an N-terminal loop works fine so I really do not get what the underlying issue might be.

I am using rosetta_bin_linux_2020.37.61417_bundle by the way

Thanks in advance,

Leonhard

[Anonymous]

So I got it to work properly by not just merging them into one singular structure (aka removing the chain ids, relabeling the residue numbers ) but also switch the order so that the missing c-terminus appears at the end of the chain. (Not suprising actual as one of course has arrived at the monomeric problem.)

I am not shure if there is a fixed version that can properly handle structures with multiple domains correctly. Otherwise, merging and reordering the multimeric structures should work for all similar cases if someone else encounters the issue.

Leonhard

 

 

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